[mira_talk] Megahubs reappearing after adding long reads
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 29 Sep 2009 18:56:03 +0200
Hi all,
I've run successfully MIRA several times, adding progressively the
results of the finishing process (shotgun libraries, and recently
fosmid libraries). At that last step, I added to my pool of Sanger
reads the results of 4 fosmid libraries. Since some of them are longer
than 20 kb, I broke the contigs into 20 kb pieces, with a 10 kb
overlap. It resulted in 10 reads.
I ran MIRA 3rc3 with or without those ten reads, and whereas the run
without these sequences is OK, I get 3 megahubs in the run with the 10
extra reads, and MIRA stops at the first pass (right after skimming).
As suggested, I tried to look into the log directory for the files
names *_int_skimmarknastyrepeats_nastyseq.0.lst, but the file is
empty. I have a file called *_int_posmatch_megahubs_preassembly.0.lst,
which gives me the names of three of the reads that I just added.
Any idea to overcome that, and why mira is finding megahubs in my long
reads? I attach the whole log file here below...
Best,
Lionel
This is MIRA V3rc3 (development version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
Mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
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http://www.chevreux.org/mira_mailinglists.html
To report bugs or ask for features, please use the new ticketing system at:
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This ensures that requests don't get lost.
Running in 64 bit mode.
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Parsing parameters: --project=BAnh1NrPeM06 -fasta
--job=denovo,genome,454,sanger,accurate -OUT:ora=yes -GE:not=4 -AS:urd=no
Parameters parsed without error, perfect.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), 454 data
Used parameter settings:
General (-GE):
Project name in (proin) : BAnh1NrPeM06
Project name out (proout) : BAnh1NrPeM06
Number of threads (not) : 4
Automatic memory management (amm) : yes
GiB memory forbidden (gbmf) : [san] 1
[454] 1
Max. process size (mps) : [san] 0
[454] 0
Keep contigs in memory (kcim) : no
EST SNP pipeline step (esps) : 1
Use template information (uti) : [san] yes
[454] yes
Template insert size minimum (tismin): [san] -1
[454] -1
Template insert size maximum (tismax): [san] -1
[454] -1
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] yes
[454] yes
File type (ft) : [san] fasta
[454] fasta
External quality (eq) : from SCF (scf)
Ext. qual. override (eqo) : no
Discard reads on e.q. error (droeqe): no
Solexa scores in qual file (ssiqf) : yes
FASTQ qual offset (fqqo) : [san] 0
[454] 0
Wants quality file (wqf) : [san] yes
[454] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[454] forward/reverse
(fr)
Merge with XML trace info (mxti) : [san] no
[454] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 5
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 3
Minimum read length (mrl) : [san] 80
[454] 40
Base default quality (bdq) : [san] 10
[454] 10
Enforce presence of qualities (epoq) : [san] yes
[454] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[454] 2
Minimum length (ardml) : [san] 400
[454] 200
Grace length (ardgl) : [san] 40
[454] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [san] 1.5
[454] 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
Load backbone (lb) : no
Start backbone usage in pass (sbuip) : 3
Backbone file type (bft) : fasta
Backbone base quality (bbq) : 30
Backbone strain name (bsn) :
Force for all (bsnffa) : no
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Also build new contigs (abnc) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [san] yes
[454] no
Read extension window length (rewl) : [san] 30
[454] 15
Read extension w. maxerrors (rewme) : [san] 2
[454] 2
First extension in pass (feip) : [san] 0
[454] 0
Last extension in pass (leip) : [san] 0
[454] 0
Clipping options (-CL):
Merge with SSAHA vector screen (msvs) : [san] no
[454] no
Gap size (msvsgs) : [san] 10
[454] 8
Max front gap (msvsmfg) : [san] 30
[454] 8
Max end gap (msvsmeg) : [san] 60
[454] 12
Strict front clip (msvssfc) : [san] 0
[454] 0
Strict end clip (msvssec) : [san] 0
[454] 0
Possible vector leftover clip (pvlc) : [san] yes
[454] no
maximum len allowed (pvcmla) : [san] 18
[454] 18
Quality clip (qc) : [san] no
[454] no
Minimum quality (qcmq) : [san] 20
[454] 20
Window length (qcwl) : [san] 30
[454] 30
Bad stretch quality clip (bsqc) : [san] yes
[454] no
Minimum quality (bsqcmq) : [san] 20
[454] 5
Window length (bsqcwl) : [san] 30
[454] 20
Masked bases clip (mbc) : [san] yes
[454] yes
Gap size (mbcgs) : [san] 20
[454] 5
Max front gap (mbcmfg) : [san] 40
[454] 12
Max end gap (mbcmeg) : [san] 60
[454] 12
Clip poly A/T at ends (cpat) : [san] no
[454] no
Keep poly-a signal (cpkps) : [san] no
[454] no
Minimum signal length (cpmsl) : [san] 12
[454] 12
Max errors allowed (cpmea) : [san] 1
[454] 1
Max gap from ends (cpmgfe) : [san] 9
[454] 9
Ensure minimum left clip (emlc) : [san] yes
[454] no
Minimum left clip req. (mlcr) : [san] 25
[454] 4
Set minimum left clip to (smlc) : [san] 30
[454] 4
Ensure minimum right clip (emrc) : [san] no
[454] no
Minimum right clip req. (mrcr) : [san] 10
[454] 10
Set minimum right clip to (smrc) : [san] 20
[454] 15
Propose end clips (pec) : yes
Bases per hash (pecbph) : 27
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 4
Bases per hash (bph) : 21
Hash save stepping (hss) : 1
Percent required (pr) : [san] 70
[454] 80
Max hits per read (mhpr) : 2000
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Max. megahub ratio (mmhr) : 0
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[454] yes
Quick rule min len 1 (qrml1) : [san] 200
[454] 80
Quick rule min sim 1 (qrms1) : [san] 90
[454] 90
Quick rule min len 2 (qrml2) : [san] 100
[454] 60
Quick rule min sim 2 (qrms2) : [san] 95
[454] 95
Backbone quick overlap min len (bqoml) : [san] 150
[454] 80
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[454] 20
Bandwidth max (bmax) : [san] 130
[454] 80
Bandwidth min (bmin) : [san] 25
[454] 20
Minimum score (ms) : [san] 30
[454] 15
Minimum overlap (mo) : [san] 15
[454] 40
Minimum relative score in % (mrs) : [san] 80
[454] 80
Solexa_hack_max_errors (shme) : [san] 0
[454] 0
Extra gap penalty (egp) : [san] no
[454] yes
extra gap penalty level (egpl) : [san] low
[454] reject_codongaps
Max. egp in percent (megpp) : [san] 100
[454] 100
Contig parameters (-CO):
Name prefix (np) : BAnh1NrPeM06
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[454] 30
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[454] 4
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[454] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[454] 25
End-read Marking Exclusion Area in bases (emea) : [san] 25
[454] 10
Also mark gap bases (amgb) : [san] yes
[454] no
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[454] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[454] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[454] no
Merge short reads (msr) : [san] no
[454] no
Gap override ratio (gor) : [san] 66
[454] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[454] yes
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Directories (-DI):
When loading EXP files :
When loading SCF files :
For writing result files : BAnh1NrPeM06_d_results
For writing result info files : BAnh1NrPeM06_d_info
For writing log files : BAnh1NrPeM06_d_log
File names (-FN):
When loading sequences from FASTA : [san]
BAnh1NrPeM06_in.sanger.fasta
[454]
BAnh1NrPeM06_in.454.fasta
When loading qualities from FASTA quality : [san]
BAnh1NrPeM06_in.sanger.fasta.qual
[454]
BAnh1NrPeM06_in.454.fasta.qual
When loading sequences from FASTQ : [san]
BAnh1NrPeM06_in.sanger.fastq
[454]
BAnh1NrPeM06_in.454.fastq
When loading project from CAF :
BAnh1NrPeM06_in.sanger.maf
When loading project from MAF (disabled) :
When loading EXP fofn : BAnh1NrPeM06_in.fofn
When loading project from PHD : BAnh1NrPeM06_in.phd.1
When loading strain data :
BAnh1NrPeM06_straindata_in.txt
When loading XML trace info files : [san]
BAnh1NrPeM06_traceinfo_in.sanger.xml
[454]
BAnh1NrPeM06_traceinfo_in.454.xml
When loading SSAHA vector screen results :
BAnh1NrPeM06_ssahavectorscreen_in.txt
When loading backbone from CAF :
BAnh1NrPeM06_backbone_in.caf
When loading backbone from GenBank :
BAnh1NrPeM06_backbone_in.gbf
When loading backbone from FASTA :
BAnh1NrPeM06_backbone_in.fasta
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[454] no
Save tagged singlets in project (stsip) : [san] yes
[454] yes
Remove rollover logs (rrol) : yes
Remove log directory (rld) : no
Result files:
Saved as CAF (orc) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : yes
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : no
Saved as wiggle (orw) : yes
Temporary result files:
Saved as CAF (otc) : yes
Saved as CAF (otm) : no
Saved as FASTA (otf) : no
Saved as GAP4 (directed assembly) (otg) : no
Saved as phrap ACE (ota) : no
Saved as HTML (oth) : no
Saved as Transposed Contig Summary (ots) : no
Saved as simple text format (ott) : no
Extended temporary result files:
Saved as CAF (oetc) : no
Saved as FASTA (oetf) : no
Saved as GAP4 (directed assembly) (oetg) : no
Saved as phrap ACE (oeta) : no
Saved as HTML (oeth) : no
Save also singlets (oetas) : no
Alignment output customisation:
TEXT characters per line (tcpl) : 60
HTML characters per line (hcpl) : 60
TEXT end gap fill character (tegfc) :
HTML end gap fill character (hegfc) :
File / directory output names:
CAF : BAnh1NrPeM06_out.caf
MAF : BAnh1NrPeM06_out.maf
FASTA : BAnh1NrPeM06_out.unpadded.fasta
FASTA quality : BAnh1NrPeM06_out.unpadded.fasta.qual
FASTA (padded) : BAnh1NrPeM06_out.padded.fasta
FASTA qual.(pad): BAnh1NrPeM06_out.padded.fasta.qual
GAP4 (directory): BAnh1NrPeM06_out.gap4da
ACE : BAnh1NrPeM06_out.ace
HTML : BAnh1NrPeM06_out.html
Simple text : BAnh1NrPeM06_out.txt
TCS overview : BAnh1NrPeM06_out.tcs
Wiggle : BAnh1NrPeM06_out.wig
------------------------------------------------------------------------------
Creating directory BAnh1NrPeM06_d_log ... done.
Creating directory BAnh1NrPeM06_d_results ... done.
Creating directory BAnh1NrPeM06_d_info ... done.
Localtime: Tue Sep 29 16:03:52 2009
Loading data (Sanger) from FASTA files,
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Found 81 sequences.
Localtime: Tue Sep 29 16:03:52 2009
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 81 reads.
Loading data (454) from FASTA files,
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Found 389391 sequences.
454 will load 389391 reads.
Longest Sanger: 20000
Longest 454: 2048
Longest Solexa: 0
Longest Solid: 0
Longest overall: 20000
Total reads to load: 389472
Reserving space for reads
Reserved space for 389482 reads.
Loading data (Sanger) from FASTA files,
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Found 81 sequences.
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Loading quality data from FASTA quality file BAnh1NrPeM06_in.sanger.fasta.qual:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Loaded 81 reads, 81 of which have quality accounted for.
Localtime: Tue Sep 29 16:04:00 2009
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.
81 SCF files were not found (see
'BAnh1NrPeM06_d_log/BAnh1NrPeM06_info_scfreadfail.0' for a list of names).
Loaded 81 Sanger reads.
Loading data (454) from FASTA files,
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Found 389391 sequences.
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Loading quality data from FASTA quality file BAnh1NrPeM06_in.454.fasta.qual:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Loaded 389391 reads, 389391 of which have quality accounted for.
Loaded 389391 454 reads.
Total reads loaded: 389472
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 1173208 kB
Buffers: 39800 kB
Cached: 4704904 kB
SwapCached: 28264 kB
Active: 3896124 kB
Inactive: 2840416 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 160 kB
Writeback: 0 kB
AnonPages: 1991368 kB
Mapped: 17984 kB
Slab: 149304 kB
SReclaimable: 133704 kB
SUnreclaim: 15600 kB
PageTables: 12104 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2332256 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 1936120 kB
VmSize: 1921428 kB
VmLck: 0 kB
VmHWM: 1933220 kB
VmRSS: 1918644 kB
VmData: 1917140 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 3768 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 663
nonvoluntary_ctxt_switches: 10102
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1937088696 (1.8 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 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_usedlogfiles: 3 112 B 0 B 0 B
Total: 1937089568 (1.8 GiB)
================================================================================
Localtime: Tue Sep 29 16:04:50 2009
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.
389472 SCF files were not found (see
'BAnh1NrPeM06_d_log/BAnh1NrPeM06_info_scfreadfail.0' for a list of names).
Localtime: Tue Sep 29 16:04:50 2009
Merging data from XML trace info file BAnh1NrPeM06_traceinfo_in.454.xml ...Num
reads: 389391
Building hash table ... done.
Localtime: Tue Sep 29 16:04:58 2009
Generated 382971 unique template ids for 389472 valid reads.
Done merging XML data, matched 389391 reads.
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.
389472 reads with valid data for assembly.
Localtime: Tue Sep 29 16:05:00 2009
Generated 382971 unique template ids for 389472 valid reads.
Localtime: Tue Sep 29 16:05:02 2009
Generated 0 unique strain ids for 389472 reads.
Strain "default" has 389472 reads.
Have read pool with 389472 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 Solexa SOLiD
---------------------------------
Total reads 81 389391 0 0
Reads wo qual 0 0 0 0
Used reads 81 388621 0 0
Avg len used 3907 303 0 0
With strain 0 0 0 0
W/o clips 0 58156 0 0
===========================================================================
Starting clips: done.
Starting minimum left clip ... done.
Performing search for bad sequence quality ... done.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 Solexa SOLiD
---------------------------------
Total reads 81 389391 0 0
Reads wo qual 0 0 0 0
Used reads 76 388621 0 0
Avg len used 3819 303 0 0
With strain 0 0 0 0
W/o clips 0 58156 0 0
===========================================================================
dmi as_init 00
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 914764 kB
Buffers: 39824 kB
Cached: 4796504 kB
SwapCached: 28264 kB
Active: 4061948 kB
Inactive: 2931996 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 8 kB
Writeback: 0 kB
AnonPages: 2157128 kB
Mapped: 18192 kB
Slab: 149792 kB
SReclaimable: 133988 kB
SUnreclaim: 15804 kB
PageTables: 12416 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2496268 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2130584 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2127840 kB
VmRSS: 2096140 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 2355
nonvoluntary_ctxt_switches: 12203
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1937088696 (1.8 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 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_usedlogfiles: 4 144 B 0 B 0 B
Total: 1937089600 (1.8 GiB)
================================================================================
dmi as_init 10
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 914808 kB
Buffers: 39824 kB
Cached: 4796440 kB
SwapCached: 28264 kB
Active: 4061948 kB
Inactive: 2931928 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 8 kB
Writeback: 0 kB
AnonPages: 2157128 kB
Mapped: 18216 kB
Slab: 149776 kB
SReclaimable: 134004 kB
SUnreclaim: 15772 kB
PageTables: 12416 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2496268 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2130584 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2127840 kB
VmRSS: 2096152 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 2355
nonvoluntary_ctxt_switches: 12206
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1937088696 (1.8 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 4 144 B 0 B 0 B
Total: 1967468448 (1.8 GiB)
================================================================================
Hash analysis for proposed cutbacks:Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Hash statistics:
=========================================================
Measured avg. frequency coverage: 56
Deduced thresholds:
-------------------
Min normal cov: 28
Max normal cov: 84
Repeat cov: 107
Crazy cov: 448
Mask cov: 0
Repeat ratio histogram:
-----------------------
0 7820168
1 2753956
2 144658
3 8522
4 946
5 212
6 84
7 14
8 22
9 8
=========================================================
Assigning values:
Localtime: Tue Sep 29 16:07:44 2009
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Tue Sep 29 16:08:28 2009
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 44743
Num reads cliped right: 161015
Num reads completely killed: 14424
Total bases clipped : 4343252
Hash analysis for proposed cutbacks:Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Hash statistics:
=========================================================
Measured avg. frequency coverage: 56
Deduced thresholds:
-------------------
Min normal cov: 28
Max normal cov: 84
Repeat cov: 107
Crazy cov: 448
Mask cov: 0
Repeat ratio histogram:
-----------------------
0 7057736
1 2753838
2 144658
3 8522
4 946
5 212
6 84
7 14
8 22
9 8
=========================================================
Assigning values:
Localtime: Tue Sep 29 16:10:54 2009
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Tue Sep 29 16:11:36 2009
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 1315
Num reads cliped right: 0
Num reads completely killed: 171
Total bases clipped : 24336
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 Solexa SOLiD
---------------------------------
Total reads 81 389391 0 0
Reads wo qual 0 0 0 0
Used reads 75 374137 0 0
Avg len used 3811 303 0 0
With strain 0 0 0 0
W/o clips 0 33356 0 0
===========================================================================
dmi pre 00
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 3756420 kB
Buffers: 11760 kB
Cached: 2028468 kB
SwapCached: 28124 kB
Active: 2837048 kB
Inactive: 1360704 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 92 kB
Writeback: 132 kB
AnonPages: 2157136 kB
Mapped: 18360 kB
Slab: 104824 kB
SReclaimable: 89196 kB
SUnreclaim: 15628 kB
PageTables: 12416 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2496480 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2451364 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2448804 kB
VmRSS: 2096284 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 100674
nonvoluntary_ctxt_switches: 26493
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1937088696 (1.8 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 4 144 B 0 B 0 B
Total: 1967468448 (1.8 GiB)
================================================================================
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Hash statistics:
=========================================================
Measured avg. frequency coverage: 60
Deduced thresholds:
-------------------
Min normal cov: 30
Max normal cov: 90
Repeat cov: 114
Crazy cov: 480
Mask cov: 6000
Repeat ratio histogram:
-----------------------
0 5831388
1 2799638
2 130682
3 8518
4 1314
5 330
6 170
7 80
8 38
9 16
10 6
=========================================================
Assigning values:
Localtime: Tue Sep 29 16:14:04 2009
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Buntifying reads ... done.
dmi pre 10
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 3774188 kB
Buffers: 11932 kB
Cached: 2009948 kB
SwapCached: 28124 kB
Active: 2836692 kB
Inactive: 1342340 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 96 kB
Writeback: 0 kB
AnonPages: 2156772 kB
Mapped: 18304 kB
Slab: 104684 kB
SReclaimable: 89412 kB
SUnreclaim: 15272 kB
PageTables: 12364 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2495872 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2451364 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2448804 kB
VmRSS: 2096308 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 144437
nonvoluntary_ctxt_switches: 30369
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2027104368 (1.9 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 5 176 B 0 B 0 B
Total: 2057484152 (1.9 GiB)
================================================================================
dmi pre 50
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 3774188 kB
Buffers: 11932 kB
Cached: 2009948 kB
SwapCached: 28124 kB
Active: 2836692 kB
Inactive: 1342340 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 96 kB
Writeback: 0 kB
AnonPages: 2156772 kB
Mapped: 18304 kB
Slab: 104684 kB
SReclaimable: 89412 kB
SUnreclaim: 15272 kB
PageTables: 12364 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2495872 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2451364 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2448804 kB
VmRSS: 2096308 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 144437
nonvoluntary_ctxt_switches: 30370
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2027104368 (1.9 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 5 176 B 0 B 0 B
Total: 2057484152 (1.9 GiB)
================================================================================
Localtime: Tue Sep 29 16:14:50 2009
Searching for possible overlaps
dmi fpo 00
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 3774188 kB
Buffers: 11932 kB
Cached: 2009948 kB
SwapCached: 28124 kB
Active: 2836692 kB
Inactive: 1342340 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 96 kB
Writeback: 0 kB
AnonPages: 2156772 kB
Mapped: 18304 kB
Slab: 104684 kB
SReclaimable: 89412 kB
SUnreclaim: 15272 kB
PageTables: 12364 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2495872 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2451364 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2448804 kB
VmRSS: 2096316 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 144438
nonvoluntary_ctxt_switches: 30372
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2027104368 (1.9 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 5 176 B 0 B 0 B
Total: 2057484152 (1.9 GiB)
================================================================================
dmi fpo 05
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 3774188 kB
Buffers: 11932 kB
Cached: 2009948 kB
SwapCached: 28124 kB
Active: 2836692 kB
Inactive: 1342340 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 96 kB
Writeback: 0 kB
AnonPages: 2156772 kB
Mapped: 18304 kB
Slab: 104684 kB
SReclaimable: 89412 kB
SUnreclaim: 15272 kB
PageTables: 12364 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2495872 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2451364 kB
VmSize: 2098828 kB
VmLck: 0 kB
VmHWM: 2448804 kB
VmRSS: 2096316 kB
VmData: 2094540 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4112 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 144438
nonvoluntary_ctxt_switches: 30373
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2027104368 (1.9 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 5 176 B 0 B 0 B
Total: 2057484152 (1.9 GiB)
================================================================================
:
Localtime: Tue Sep 29 16:14:50 2009
Now running threaded and partitioned skimmer with 8 partitions in 4 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
Skim summary:
accepted: 22392467
possible: 29509493
permbans: 0
Hits chosen: 22392467
Localtime: Tue Sep 29 16:32:50 2009
Total megahubs: 3
dmi fpo 10
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8113380 kB
MemFree: 2862848 kB
Buffers: 12392 kB
Cached: 2617968 kB
SwapCached: 28124 kB
Active: 3140124 kB
Inactive: 1950020 kB
SwapTotal: 8385920 kB
SwapFree: 8299932 kB
Dirty: 0 kB
Writeback: 0 kB
AnonPages: 2459432 kB
Mapped: 18376 kB
Slab: 104796 kB
SReclaimable: 89248 kB
SUnreclaim: 15548 kB
PageTables: 13028 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 12442608 kB
Committed_AS: 2862800 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 305308 kB
VmallocChunk: 34359429383 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 6148 kB
DirectMap2M: 8314880 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22354
Pid: 22354
PPid: 1
TracerPid: 0
Uid: 1166 1166 1166 1166
Gid: 100 100 100 100
FDSize: 256
Groups: 100 1001 1002 1003 1004 1006
VmPeak: 2880280 kB
VmSize: 2596248 kB
VmLck: 0 kB
VmHWM: 2633536 kB
VmRSS: 2398972 kB
VmData: 2591960 kB
VmStk: 84 kB
VmExe: 4168 kB
VmLib: 0 kB
VmPTE: 4768 kB
Threads: 1
SigQ: 0/73216
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000006
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Cpus_allowed_list: 0-7
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 145628
nonvoluntary_ctxt_switches: 31691
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 389472 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2027104368 (1.9 GiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 389472 1 MiB 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 18 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: 389472 1 MiB 0 B 0 B
AS_clipright: 389472 1 MiB 0 B 0 B
AS_used_ids: 389472 380 KiB 0 B 0 B
AS_multicopies: 0 380 KiB 380 KiB 0 B
AS_hasmcoverlaps: 0 380 KiB 380 KiB 0 B
AS_maxcoveragereached: 389472 1 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 389472 380 KiB 0 B 0 B
AS_isdebris: 389472 380 KiB 0 B 0 B
AS_needalloverlaps: 389472 380 KiB 32 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 1 MiB 1 MiB 0 B
AS_probablermbsnotok: 0 1 MiB 1 MiB 0 B
AS_weakrmbsnotok: 0 1 MiB 1 MiB 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_usedlogfiles: 10 336 B 0 B 0 B
Total: 2059042200 (1.9 GiB)
================================================================================
MIRA has detected megahubs in your data.This may not be a problem, but most
probably is, especially for eukaryotes.
You have more than 0.0% of your reads found to be megahubs.
You should sheck the following:
1) for Sanger sequences: are all the sequencing vectors masked /
clipped?
2) for 454 sequences: are all the adaptors masked / clipped?
You will find in the log directory a file called
'mira_int_skimmarknastyrepeats_nastyseq_*',
consult the MIRA manual on how to extract reapeat information from there.
*ONLY* when you are sure that no (or only a very negligible number) of
sequencing
vector / adaptor sequence is remaining, try this:
3) for organisms with complex repeats (eukaryots & some bacteria):
- reduce the -SK:nrr parameter (divide by 2)
) for EST projects, -SK:nrr will not really work, use -SK:rt (increasing it in
steps of 2)
*ONLY* if the above fails, try increasing the -SK:mmhr parameter
You have 0.0% of your reads as megahubs.
You have set a maximum allowed ratio of: 0.0
Ending the assembly because the maximum ratio has been reached/surpassed.
============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala
phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
============================================
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