[mira_talk] What is this referring to?

  • From: Rob Good <rtgood@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 5 May 2011 16:35:52 +1000

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."

->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.

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        http://www.chevreux.org/mira_mailinglists.html

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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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