[mira_talk] Re: What is this referring to?

  • From: Ganga Jeena <ganga.jeena@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 5 May 2011 13:52:59 +0530

On Thu, May 5, 2011 at 12:05 PM, Rob Good <rtgood@xxxxxxxxxxxxxx> wrote:

> I have done a de novo assembly with SOAPdenovo and am now aligning it to
> the reference strain with mira.
> I broke all the contigs greater than 10k up but I'm getting this error and
> don't know what it is referring to ...
> Can someone enlighten me please???
>
>
>
> Fatal error (may be due to problems of the input data or parameters):
>

*>"Read rr_####2568#### is longer than MAXREADSIZEALLOWED (29900) bases.
Skim cannot handle than, sorry."*
makes it seem as if there are still few contigs with size > 29900. checkout
for the same and split again.
Regards,
Ganga Jeena

>
> ->Thrown: void Skim::transformSeqToVariableHash (...)
> ->Caught: main
>
> Aborting process, probably due to error in the input data or
> parametrisation.
> Please check the output log for more information.
>
> The full log is below
>
> Rob Good
> Ph. +61 3 8344 2347
> Mob. 0434058250
> Genetics Dept
> University of Melbourne
> PARKVILLE, Australia
>
>
> This is MIRA V3.2.1 (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:
>        http://www.chevreux.org/mira_mailinglists.html
>
> After subscribing, mail general questions to the MIRA talk mailing list:
>        mira_talk@xxxxxxxxxxxxx
>
> 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 by: bjpop
> Wed Dec  8 16:18:25 EST 2010
> On: Linux bruce-m.vlsci.unimelb.edu.au 2.6.18-164.11.1.el5 #1 SMP Wed Jan
> 20 07:32:21 EST 2010 x86_64 x86_64 x86_64 GNU/Linux
> Compiled in boundtracking mode.
> Compiled in bugtracking mode.
> Compilation 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 bruce118 2.6.18-238.5.1.el5 #1 SMP Fri Apr 1 18:41:58
> EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
>
>
>
> Parsing parameters: --project=DGRP-712 --job=genome,sanger,mapping,accurate
> -SK:not=8 SANGER_SETTINGS -LR:wqf=no -AS:epoq=no
>
>
>
>
> 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)
>
> Used parameter settings:
>  General (-GE):
>        Project name in (proin)                     : DGRP-712
>        Project name out (proout)                   : DGRP-712
>        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)              : yes
>            Template insert size minimum (tismin)   : -1
>            Template insert size maximum (tismax)   : -1
>            Template partner build direction (tpbd) : -1
>        Colour reads by hash frequency (crhf)       : yes
>
>  Load reads options (-LR):
>        Load sequence data (lsd)                    : yes
>            File type (ft)                          : 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)      : no
>            FASTQ qual offset (fqqo)                : 0
>
>        Wants quality file (wqf)                    : no
>
>        Read naming scheme (rns)                    :  [san] Sanger
> Institute (sanger)
>
>        Merge with XML trace info (mxti)            : no
>
>        Filecheck only (fo)                         : no
>
>  Assembly options (-AS):
>        Number of passes (nop)                      : 1
>            Skim each pass (sep)                    : yes
>        Maximum number of RMB break loops (rbl)     : 1
>
>        Minimum read length (mrl)                   : 80
>        Minimum reads per contig (mrpc)             : 2
>        Base default quality (bdq)                  : 10
>        Enforce presence of qualities (epoq)        : no
>
>        Automatic repeat detection (ard)            : yes
>            Coverage threshold (ardct)              : 2
>            Minimum length (ardml)                  : 400
>            Grace length (ardgl)                    : 40
>            Use uniform read distribution (urd)     : no
>              Start in pass (urdsip)                : 3
>              Cutoff multiplier (urdcm)             : 1.5
>        Keep long repeats separated (klrs)          : no
>
>        Spoiler detection (sd)                      : yes
>            Last pass only (sdlpo)                  : yes
>
>        Use genomic pathfinder (ugpf)               : yes
>
>        Use emergency search stop (uess)            : yes
>            ESS partner depth (esspd)               : 500
>        Use emergency blacklist (uebl)              : yes
>        Use max. contig build time (umcbt)          : no
>            Build time in seconds (bts)             : 10000
>
>  Strain and backbone options (-SB):
>        Load straindata (lsd)                       : no
>        Assign default strain (ads)                 : yes
>            Default strain name (dsn)               : StrainX
>        Load backbone (lb)                          : yes
>            Start backbone usage in pass (sbuip)    : 0
>            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)           : no
>
>  Dataprocessing options (-DP):
>        Use read extensions (ure)                   : yes
>            Read extension window length (rewl)     : 30
>            Read extension w. maxerrors (rewme)     : 2
>            First extension in pass (feip)          : 0
>            Last extension in pass (leip)           : 0
>
>  Clipping options (-CL):
>        Merge with SSAHA2/SMALT vector screen (msvs): no
>            Gap size (msvsgs)                       : 10
>            Max front gap (msvsmfg)                 : 60
>            Max end gap (msvsmeg)                   : 120
>            Strict front clip (msvssfc)             : 0
>            Strict end clip (msvssec)               : 0
>        Possible vector leftover clip (pvlc)        : yes
>            maximum len allowed (pvcmla)            : 18
>        Quality clip (qc)                           : no
>            Minimum quality (qcmq)                  : 20
>            Window length (qcwl)                    : 30
>        Bad stretch quality clip (bsqc)             : yes
>            Minimum quality (bsqcmq)                : 20
>            Window length (bsqcwl)                  : 30
>        Masked bases clip (mbc)                     : yes
>            Gap size (mbcgs)                        : 20
>            Max front gap (mbcmfg)                  : 40
>            Max end gap (mbcmeg)                    : 60
>        Lower case clip (lcc)                       : no
>        Clip poly A/T at ends (cpat)                : no
>            Keep poly-a signal (cpkps)              : no
>            Minimum signal length (cpmsl)           : 12
>            Max errors allowed (cpmea)              : 1
>            Max gap from ends (cpmgfe)              : 9
>        Ensure minimum left clip (emlc)             : yes
>            Minimum left clip req. (mlcr)           : 25
>            Set minimum left clip to (smlc)         : 30
>        Ensure minimum right clip (emrc)            : no
>            Minimum right clip req. (mrcr)          : 10
>            Set minimum right clip to (smrc)        : 20
>
>        Apply SKIM chimera detection clip (ascdc)   : yes
>        Apply SKIM junk detection clip (asjdc)      : no
>
>        Propose end clips (pec)                     : yes
>            Bases per hash (pecbph)                 : 17
>            Handle Solexa GGCxG problem (pechsgp)   : yes
>
>  Parameters for SKIM algorithm (-SK):
>        Number of threads (not)                     : 8
>
>        Also compute reverse complements (acrc)     : yes
>        Bases per hash (bph)                        : 16
>        Hash save stepping (hss)                    : 4
>        Percent required (pr)                       : 60
>
>        Max hits per read (mhpr)                    : 1000
>        Max megahub ratio (mmhr)                    : 0
>
>        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)                    : no
>            Nasty repeat ratio (nrr)                : 100
>        Repeat level in info file (rliif)           : 6
>
>        Max hashes in memory (mhim)                 : 15000000
>        MemCap: hit reduction (mchr)                : 2048
>
>  Pathfinder options (-PF):
>        Use quick rule (uqr)                        : yes
>            Quick rule min len 1 (qrml1)            : 200
>            Quick rule min sim 1 (qrms1)            : 90
>            Quick rule min len 2 (qrml2)            : 100
>            Quick rule min sim 2 (qrms2)            : 95
>        Backbone quick overlap min len (bqoml)      : 150
>
>  Align parameters for Smith-Waterman align (-AL):
>        Bandwidth in percent (bip)             : 20
>        Bandwidth max (bmax)                   : 130
>        Bandwidth min (bmin)                   : 25
>        Minimum score (ms)                     : 30
>        Minimum overlap (mo)                   : 15
>        Minimum relative score in % (mrs)      : 65
>        Solexa_hack_max_errors (shme)          : 0
>        Extra gap penalty (egp)                : no
>            extra gap penalty level (egpl)     :  [san] low
>            Max. egp in percent (megpp)        : 100
>
>  Contig parameters (-CO):
>        Name prefix (np)                                         : DGRP-712
>        Reject on drop in relative alignment score in % (rodirs) : 25
>        Mark repeats (mr)                                        : yes
>            Only in result (mroir)                               : no
>            Assume SNP instead of repeats (asir)                 : no
>            Minimum reads per group needed for tagging (mrpg)    : 2
>            Minimum neighbour quality needed for tagging (mnq)   : 20
>            Minimum Group Quality needed for RMB Tagging (mgqrt) : 30
>            End-read Marking Exclusion Area in bases (emea)      : 1
>                Set to 1 on clipping PEC (emeas1clpec)           : yes
>            Also mark gap bases (amgb)                           : yes
>                Also mark gap bases - even multicolumn (amgbemc) : yes
>                Also mark gap bases - need both strands (amgbnbs): yes
>        Force non-IUPAC consensus per sequencing type (fnicpst)  : no
>        Merge short reads (msr)                                  : no
>        Gap override ratio (gor)                                 : 66
>
>  Edit options (-ED):
>        Automatic contig editing (ace)              : no
>     Sanger only:
>        Strict editing mode (sem)                   : no
>        Confirmation threshold in percent (ct)      : 50
>
>  Misc (-MI):
>        Stop on NFS (sonfs)                         : yes
>        Large contig size (lcs)                     : 500
>        Large contig size for stats(lcs4s)          : 5000
>
>  Directories (-DI):
>        When loading EXP files            :
>        When loading SCF files            :
>        Top directory for writing files   : DGRP-712_assembly
>        For writing result files          :
> DGRP-712_assembly/DGRP-712_d_results
>        For writing result info files     :
> DGRP-712_assembly/DGRP-712_d_info
>        For writing log files             : DGRP-712_assembly/DGRP-712_d_log
>        Log redirected to (lrt)           :
>        For writing checkpoint files      :
> DGRP-712_assembly/DGRP-712_d_chkpt
>
>  File names (-FN):
>        When loading sequences from FASTA            :
> DGRP-712_in.sanger.fasta
>        When loading qualities from FASTA quality    :
> DGRP-712_in.sanger.fasta.qual
>        When loading sequences from FASTQ            :
> DGRP-712_in.sanger.fastq
>        When loading project from CAF                :
> DGRP-712_in.sanger.caf
>        When loading project from MAF (disabled)     :
> DGRP-712_in.sanger.maf
>        When loading EXP fofn                        :
> DGRP-712_in.sanger.fofn
>        When loading project from PHD                : DGRP-712_in.phd.1
>        When loading strain data                     :
> DGRP-712_straindata_in.txt
>        When loading XML trace info files            :
> DGRP-712_traceinfo_in.sanger.xml
>        When loading SSAHA2 vector screen results    :
> DGRP-712_ssaha2vectorscreen_in.txt
>        When loading SMALT vector screen results     :
> DGRP-712_smaltvectorscreen_in.txt
>
>        When loading backbone from MAF               :
> DGRP-712_backbone_in.maf
>        When loading backbone from CAF               :
> DGRP-712_backbone_in.caf
>        When loading backbone from GenBank           :
> DGRP-712_backbone_in.gbf
>        When loading backbone from FASTA             :
> DGRP-712_backbone_in.fasta
>
>
>  Output files (-OUTPUT/-OUT):
>        Save simple singlets in project (sssip)      : no
>        Save tagged singlets in project (stsip)      : yes
>
>        Remove rollover logs (rrol)                  : yes
>        Remove log directory (rld)                   : 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 HTML                      (orh)     : no
>        Saved as Transposed Contig Summary (ors)     : yes
>        Saved as simple text format        (ort)     : no
>        Saved as wiggle                    (orw)     : yes
>
>    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             : DGRP-712_out.caf
>        MAF             : DGRP-712_out.maf
>        FASTA           : DGRP-712_out.unpadded.fasta
>        FASTA quality   : DGRP-712_out.unpadded.fasta.qual
>        FASTA (padded)  : DGRP-712_out.padded.fasta
>        FASTA qual.(pad): DGRP-712_out.padded.fasta.qual
>        GAP4 (directory): DGRP-712_out.gap4da
>        ACE             : DGRP-712_out.ace
>        HTML            : DGRP-712_out.html
>        Simple text     : DGRP-712_out.txt
>        TCS overview    : DGRP-712_out.tcs
>        Wiggle          : DGRP-712_out.wig
>
> ------------------------------------------------------------------------------
> Deleting old directory DGRP-712_assembly ... done.
> Creating directory DGRP-712_assembly ... done.
> Creating directory DGRP-712_assembly/DGRP-712_d_log ... done.
> Creating directory DGRP-712_assembly/DGRP-712_d_results ... done.
> Creating directory DGRP-712_assembly/DGRP-712_d_info ... done.
> Creating directory DGRP-712_assembly/DGRP-712_d_chkpt ... done.
>
> Log directory is not on a NFS mount, good.
>
> Localtime: Thu May  5 16:07:06 2011
>
> Loading backbone from FASTA file: DGRP-712_backbone_in.fasta (quality:
> DGRP-712_backbone_in.fasta.qual)
> Localtime: Thu May  5 16:07:06 2011
> Counting sequences in FASTA file:
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Found 15 sequences.
> Localtime: Thu May  5 16:07:10 2011
> Loading data from FASTA file:
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Localtime: Thu May  5 16:07:15 2011
> rnm size: 0
> Could not find FASTA quality file DGRP-712_backbone_in.fasta.qual, using
> default values for these reads.
> Localtime: Thu May  5 16:07:15 2011
>
> Done.
> Loaded 15 reads with 168736537 raw bases.
> 0 reads have quality accounted for.
> Postprocessing backbone(s) ... this may take a while.
> 15 to process
> 2L_bb   23011544
> 2LHet_bb        368872
> 2R_bb   21146708
> 2RHet_bb        3288761
> 3L_bb   24543557
> 3LHet_bb        2555491
> 3R_bb   27905053
> 3RHet_bb        2517507
> 4_bb    1351857
> M_bb    19517
> Uextra_bb       29004656
> U_bb    10049037
> X_bb    22422827
> XHet_bb 204112
> YHet_bb 347038
> Localtime: Thu May  5 16:07:24 2011
>
> Seeing strain 1: "ReferenceStrain"
> Generated 1 unique strain ids for 15 reads.
> Strain "default" has 0 reads.
> Strain "ReferenceStrain" has 15 reads.
> Loading data (Sanger) from FASTA files,
> Localtime: Thu May  5 16:07:24 2011
> Counting sequences in FASTA file:
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Found 61411 sequences.
> Localtime: Thu May  5 16:07:31 2011
> Localtime: Thu May  5 16:07:31 2011
>
> Checking SCF files (loading qualities only if needed):
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Done.
> 0 SCF files loaded ok.
>
>
> Sanger will load 61411 reads.
> Longest Sanger: 10000
> Longest 454: 0
> Longest PacBio: 0
> Longest Solexa: 0
> Longest Solid: 0
> Longest overall: 10000
> Total reads to load: 61411
> -SB:brl is 0, automatically determining optimal value.
> Optimal rail would be longer than 18k, adjusting down to 18k.
> brl: 18000
> -SB:bro is 0, automatically determining optimal value.
> bro: 9000
> Reserving space for reads
> Reserved space for 80147 reads (including backbone rails).
> Adding rails to 15 contigs (this may take a while).
> Loading data (Sanger) from FASTA files,
> Localtime: Thu May  5 16:09:45 2011
> Counting sequences in FASTA file:
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Found 61411 sequences.
> Localtime: Thu May  5 16:09:48 2011
> Loading data from FASTA file:
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|..
> Warning: C1530710_1 has no bases?! This usually points at some error in the
> processing of data before it arrives to MIRA.
> .. [100%]
> Localtime: Thu May  5 16:09:52 2011
> rnm size: 0
> Could not find FASTA quality file DGRP-712_in.sanger.fasta.qual, using
> default values for these reads.
> Localtime: Thu May  5 16:09:53 2011
>
> Done.
> Loaded 61411 reads with 129557687 raw bases.
> 0 reads have quality accounted for.
> Localtime: Thu May  5 16:09:53 2011
>
> Checking SCF files (loading qualities only if needed):
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Done.
> 0 SCF files loaded ok.
> 61410 SCF files were not found (see
> 'DGRP-712_assembly/DGRP-712_d_log/DGRP-712_info_scfreadfail.0' for a list of
> names).
>
>
> Loaded 61411 Sanger reads.
> Total reads loaded: 61411
> Localtime: Thu May  5 16:09:58 2011
>
> Checking SCF files (loading qualities only if needed):
>  [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Done.
> 0 SCF files loaded ok.
> 61410 SCF files were not found (see
> 'DGRP-712_assembly/DGRP-712_d_log/DGRP-712_info_scfreadfail.0' for a list of
> names).
>
>
> 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.
> 80136 reads with valid data for assembly.
> Localtime: Thu May  5 16:09:59 2011
>
> Generated 80136 unique template ids for 80136 valid reads.
> No useful template information found, template routines will not be used.
> Localtime: Thu May  5 16:09:59 2011
>
> Seeing strain 1: "ReferenceStrain"
> Seeing strain 2: "StrainX"
> Generated 2 unique strain ids for 80137 reads.
> Strain "default" has 1 reads.
> Strain "ReferenceStrain" has 15 reads.
> Strain "StrainX" has 61410 reads.
> Have read pool with 80137 reads.
> C1530710_1: unable to load or other reason for invalid data.
>
> ===========================================================================
> Pool statistics:
> Backbones: 15   Backbone rails: 18711
>
>                Sanger  454     PacBio  Solexa  SOLiD
>                ----------------------------------------
> Total reads     61411   0       0       0       0
> Reads wo qual   61411   0       0       0       0
> Used reads      61361   0       0       0       0
> Avg tot rlen    2109    0       0       0       0
> Avg rlen used   2111    0       0       0       0
>
> With strain     61411   0       0       0       0
> W/o clips       0       0       0       0       0
> ===========================================================================
>
>
> Starting clips:  done.
> Clipping: requested bad sequence search clip and a minimum left clip
> Need to perform minimum left clip before bad sequence search clip.
> Starting minimum left clip ... done.
> Performing search for bad sequence quality ... done.
> C1530710_1: unable to load or other reason for invalid data.
>
> ===========================================================================
> Pool statistics:
> Backbones: 15   Backbone rails: 18711
>
>                Sanger  454     PacBio  Solexa  SOLiD
>                ----------------------------------------
> Total reads     61411   0       0       0       0
> Reads wo qual   61411   0       0       0       0
> Used reads      56244   0       0       0       0
> Avg tot rlen    2109    0       0       0       0
> Avg rlen used   2263    0       0       0       0
>
> With strain     61411   0       0       0       0
> W/o clips       0       0       0       0       0
> ===========================================================================
>
>
>
> Log directory is not on a NFS mount, good.
>
> Hash analysis for proposed cutbacks:Localtime: Thu May  5 16:10:01 2011
> Writing temporary hstat files:
>  [0%] ...
>
> ========================== Memory self assessment
> ==============================
> Running in 64 bit mode.
>
> Dump from /proc/meminfo
>
> --------------------------------------------------------------------------------
> MemTotal:     49448756 kB
> MemFree:      16608868 kB
> Buffers:        298124 kB
> Cached:       13490800 kB
> SwapCached:          0 kB
> Active:       19048504 kB
> Inactive:     13374404 kB
> HighTotal:           0 kB
> HighFree:            0 kB
> LowTotal:     49448756 kB
> LowFree:      16608868 kB
> SwapTotal:    10482404 kB
> SwapFree:     10482404 kB
> Dirty:          320772 kB
> Writeback:         292 kB
> AnonPages:    18634020 kB
> Mapped:          15488 kB
> Slab:           247892 kB
> PageTables:      39756 kB
> NFS_Unstable:        0 kB
> Bounce:              0 kB
> CommitLimit:  56469744 kB
> Committed_AS: 18802392 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed:    278268 kB
> VmallocChunk: 34359434479 kB
> HugePages_Total:     0
> HugePages_Free:      0
> HugePages_Rsvd:      0
> Hugepagesize:     2048 kB
>
> --------------------------------------------------------------------------------
>
> Dump from /proc/self/status
>
> --------------------------------------------------------------------------------
> Name:   mira
> State:  R (running)
> SleepAVG:       77%
> Tgid:   4568
> Pid:    4568
> PPid:   4565
> TracerPid:      0
> Uid:    610     610     610     610
> Gid:    522     522     522     522
> FDSize: 256
> Groups: 522
> VmPeak: 18182660 kB
> VmSize: 18182660 kB
> VmLck:         0 kB
> VmHWM:  18154484 kB
> VmRSS:  18154484 kB
> VmData: 18154632 kB
> VmStk:        92 kB
> VmExe:      3000 kB
> VmLib:      4312 kB
> VmPTE:     35584 kB
> StaBrk: 00916000 kB
> Brk:    3b3ed1000 kB
> StaStk: 7fffffffdb10 kB
> Threads:        1
> SigQ:   0/401408
> SigPnd: 0000000000000000
> ShdPnd: 0000000000000000
> SigBlk: 0000000000000000
> SigIgn: 0000000000001000
> SigCgt: 0000000180000000
> CapInh: 0000000000000000
> CapPrm: 0000000000000000
> CapEff: 0000000000000000
> Cpus_allowed:
> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000008
> Mems_allowed:   00000000,00000003
>
> --------------------------------------------------------------------------------
>
> Information on current assembly object:
>
> AS_readpool: 80137 reads.
> AS_contigs: 0 contigs.
> AS_bbcontigs: 15 contigs.
> Mem used for reads: 5743048088 (5.3 GiB)
>
> 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:          0       4 MiB         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:      80137     313 KiB         0 B         4 B
>                AS_clipright:      80137     313 KiB         0 B         4 B
>                 AS_used_ids:      80137      78 KiB         0 B         7 B
>              AS_multicopies:          0      78 KiB      78 KiB         7 B
>            AS_hasmcoverlaps:          0      78 KiB      78 KiB         7 B
>       AS_maxcoveragereached:      80137     313 KiB         0 B         4 B
>       AS_coverageperseqtype:          0        24 B         0 B         0 B
>           AS_istroublemaker:      80137      78 KiB         0 B         7 B
>                 AS_isdebris:      80137      78 KiB         0 B         7 B
>          AS_needalloverlaps:      80137      78 KiB        55 B         0 B
>    AS_readsforrepeatresolve:          0        40 B         0 B         0 B
>                AS_allrmbsok:          0     313 KiB     313 KiB         4 B
>        AS_probablermbsnotok:          0     313 KiB     313 KiB         4 B
>            AS_weakrmbsnotok:          0     313 KiB     313 KiB         4 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_usedlogfiles:          4       144 B         0 B         0 B
> Total: 5749299792 (5.4 GiB)
>
>
> ================================================================================
> Dynamic allocs: 0
> Align allocs: 0
>
> Fatal error (may be due to problems of the input data or parameters):
>
> "Read rr_####2568#### is longer than MAXREADSIZEALLOWED (29900) bases. Skim
> cannot handle than, sorry."
>
> ->Thrown: void Skim::transformSeqToVariableHash (...)
> ->Caught: main
>
> Aborting process, probably due to error in the input data or
> parametrisation.
> Please check the output log for more information.
> For help, please write a mail to the mira talk mailing list.
>
> CWD: /vlsci/VR0013/rtgood/data/712soap
> Thank you for noticing that this is *NOT* a crash, but a
> controlled program stop.
>
>
> --
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> visit http://www.chevreux.org/mira_mailinglists.html
>

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