[mira_talk] internal logic… error
- From: "Langhorst, Brad" <Langhorst@xxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 15 Oct 2012 13:14:38 +0000
I'd like to report this error we just ran across during an assembly.
This looks like the same error reported in ticket #85
https://sourceforge.net/apps/trac/mira-assembler/ticket/85
Any suggestions?
I plan to install a more recent version of Mira, but I need to do some work on
the galaxy wrappers to make it useful for us - so I won't get to that for a
while.
The "reference" contains 8 contigs
>SequenceA
>SequenceB
…
here is the mira log:
This is MIRA V3.4.0 (production version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
To (un-)subscribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
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mira_talk@xxxxxxxxxxxxx<mailto:mira_talk@xxxxxxxxxxxxx>
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This ensures that requests don't get lost.
Compiled by: bach
Sun Aug 21 17:50:30 CEST 2011
On: Linux arcadia 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC 2011
x86_64 x86_64 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux seq03-i 2.6.32-28-server #55-Ubuntu SMP Mon Jan 10
23:57:16 UTC 2011 x86_64 GNU/Linux
Parsing parameters: --job=denovo,genome,draft -SB:lb=1:bft=fasta
-FN:bbin=/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
SOLEXA_SETTINGS -LR:lsd=1:ft=fastq
-FN:fqi=/mnt/ngswork/galaxy/galaxy-dist/database/files/023/dataset_23893.dat
-CO:msr=0 -GE:uti=0:tismin=-1:tismax=-1 COMMON_SETTINGS -MI:somrnl=0
-DI:trt=/mnt/ngswork/tmp -MI:sonfs=no
-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1
-SB:sbuip is 3, but must be no more than 2. Setting to 2
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), Solexa data
Used parameter settings:
General (-GE):
Project name in (proin) : mira
Project name out (proout) : mira
Number of threads (not) : 2
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[sxa] no
Template insert size minimum (tismin) : [san] -1
[sxa] -1
Template insert size maximum (tismax) : [san] -1
[sxa] -1
Template partner build direction (tpbd) : [san] -1
[sxa] -1
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] no
[sxa] yes
File type (ft) : [san] fasta
[sxa] fastq
External quality (eq) : from SCF (scf)
Ext. qual. override (eqo) : no
Discard reads on e.q. error (droeqe): no
Solexa scores in qual file (ssiqf) : no
FASTQ qual offset (fqqo) : [san] 0
[sxa] 0
Wants quality file (wqf) : [san] yes
[sxa] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[sxa] Solexa (solexa)
Merge with XML trace info (mxti) : [san] no
[sxa] no
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 2
Skim each pass (sep) : no
Maximum number of RMB break loops (rbl) : 1
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [san] 80
[sxa] 20
Minimum reads per contig (mrpc) : [san] 2
[sxa] 10
Base default quality (bdq) : [san] 10
[sxa] 10
Enforce presence of qualities (epoq) : [san] yes
[sxa] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[sxa] 2.5
Minimum length (ardml) : [san] 400
[sxa] 300
Grace length (ardgl) : [san] 40
[sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [san] 1.5
[sxa] 1.5
Keep long repeats separated (klrs) : no
Spoiler detection (sd) : no
Last pass only (sdlpo) : yes
Use genomic pathfinder (ugpf) : 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) : [san] no
[sxa] no
Default strain name (dsn) : [san] StrainX
[sxa] StrainX
Load backbone (lb) : yes
Start backbone usage in pass (sbuip) : 2
Backbone file type (bft) : fasta
Backbone base quality (bbq) : 30
Backbone strain name (bsn) : ReferenceStrain
Force for all (bsnffa) : no
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Also build new contigs (abnc) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [san] no
[sxa] no
Read extension window length (rewl) : [san] 30
[sxa] 30
Read extension w. maxerrors (rewme) : [san] 2
[sxa] 2
First extension in pass (feip) : [san] 0
[sxa] 0
Last extension in pass (leip) : [san] 0
[sxa] 0
Clipping options (-CL):
Merge with SSAHA2/SMALT vector screen (msvs): [san] no
[sxa] no
Gap size (msvsgs) : [san] 10
[sxa] 1
Max front gap (msvsmfg) : [san] 60
[sxa] 2
Max end gap (msvsmeg) : [san] 120
[sxa] 2
Strict front clip (msvssfc) : [san] 0
[sxa] 0
Strict end clip (msvssec) : [san] 0
[sxa] 0
Possible vector leftover clip (pvlc) : [san] no
[sxa] no
maximum len allowed (pvcmla) : [san] 18
[sxa] 18
Min qual. threshold for entire read (mqtfer): [san] 0
[sxa] 5
Number of bases (mqtfernob) : [san] 0
[sxa] 15
Quality clip (qc) : [san] no
[sxa] no
Minimum quality (qcmq) : [san] 20
[sxa] 20
Window length (qcwl) : [san] 30
[sxa] 30
Bad stretch quality clip (bsqc) : [san] yes
[sxa] no
Minimum quality (bsqcmq) : [san] 20
[sxa] 5
Window length (bsqcwl) : [san] 30
[sxa] 20
Masked bases clip (mbc) : [san] yes
[sxa] no
Gap size (mbcgs) : [san] 20
[sxa] 5
Max front gap (mbcmfg) : [san] 40
[sxa] 12
Max end gap (mbcmeg) : [san] 60
[sxa] 12
Lower case clip (lcc) : [san] no
[sxa] no
Clip poly A/T at ends (cpat) : [san] no
[sxa] no
Keep poly-a signal (cpkps) : [san] no
[sxa] no
Minimum signal length (cpmsl) : [san] 12
[sxa] 12
Max errors allowed (cpmea) : [san] 1
[sxa] 1
Max gap from ends (cpmgfe) : [san] 9
[sxa] 9
Clip 3 prime polybase (c3pp) : [san] no
[sxa] yes
Minimum signal length (c3ppmsl) : [san] 12
[sxa] 12
Max errors allowed (c3ppmea) : [san] 2
[sxa] 2
Max gap from ends (c3ppmgfe) : [san] 9
[sxa] 9
Clip known adaptors right (ckar) : [san] no
[sxa] yes
Ensure minimum left clip (emlc) : [san] yes
[sxa] no
Minimum left clip req. (mlcr) : [san] 25
[sxa] 0
Set minimum left clip to (smlc) : [san] 30
[sxa] 0
Ensure minimum right clip (emrc) : [san] no
[sxa] no
Minimum right clip req. (mrcr) : [san] 10
[sxa] 10
Set minimum right clip to (smrc) : [san] 20
[sxa] 20
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : yes
Bases per hash (pecbph) : 17
Handle Solexa GGCxG problem (pechsgp) : yes
Clip bad solexa ends (cbse) : yes
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 2
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 17
Hash save stepping (hss) : 8
Percent required (pr) : [san] 70
[sxa] 90
Max hits per read (mhpr) : 200
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : no
Freq. est. min normal (fenn) : 0.4
Freq. est. max normal (fexn) : 1.6
Freq. est. repeat (fer) : 1.9
Freq. est. heavy repeat (fehr) : 8
Freq. est. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Repeat level in info file (rliif) : 6
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[sxa] yes
Quick rule min len 1 (qrml1) : [san] 200
[sxa] -95
Quick rule min sim 1 (qrms1) : [san] 90
[sxa] 100
Quick rule min len 2 (qrml2) : [san] 100
[sxa] -85
Quick rule min sim 2 (qrms2) : [san] 95
[sxa] 100
Backbone quick overlap min len (bqoml) : [san] 150
[sxa] 20
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 15
[sxa] 20
Bandwidth max (bmax) : [san] 70
[sxa] 80
Bandwidth min (bmin) : [san] 25
[sxa] 20
Minimum score (ms) : [san] 30
[sxa] 15
Minimum overlap (mo) : [san] 17
[sxa] 25
Minimum relative score in % (mrs) : [san] 65
[sxa] 90
Solexa_hack_max_errors (shme) : [san] 0
[sxa] 0
Extra gap penalty (egp) : [san] no
[sxa] no
extra gap penalty level (egpl) : [san] low
[sxa] low
Max. egp in percent (megpp) : [san] 100
[sxa] 100
Contig parameters (-CO):
Name prefix (np) : mira
Reject on drop in relative alignment score in % (rodirs) : [san] 15
[sxa] 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
[sxa] 4
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[sxa] 30
End-read Marking Exclusion Area in bases (emea) : [san] 1
[sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[sxa] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[sxa] no
Merge short reads (msr) : [san] no
[sxa] no
Keep ends unmerged (msrkeu) : [san] -1
[sxa] -1
Gap override ratio (gor) : [san] 66
[sxa] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[sxa] no
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Misc (-MI):
Stop on NFS (sonfs) : no
Extended log (el) : no
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 5000
Stop on max read name length (somrnl) : 0
Directories (-DI):
Working directory :
When loading EXP files :
When loading SCF files :
Top directory for writing files : mira_assembly
For writing result files : mira_assembly/mira_d_results
For writing result info files : mira_assembly/mira_d_info
For writing tmp files : /mnt/ngswork/tmp/mira_d_tmp
Tmp redirected to (trt) : /mnt/ngswork/tmp
For writing checkpoint files : mira_assembly/mira_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
mira_in.sanger.fasta
[sxa]
mira_in.solexa.fasta
When loading qualities from FASTA quality : [san]
mira_in.sanger.fasta.qual
[sxa]
mira_in.solexa.fasta.qual
When loading sequences from FASTQ : [san]
mira_in.sanger.fastq
[sxa]
/mnt/ngswork/galaxy/galaxy-dist/database/files/023/dataset_23893.dat
When loading project from CAF : mira_in.sanger.caf
When loading project from MAF (disabled) : mira_in.sanger.maf
When loading EXP fofn : mira_in.sanger.fofn
When loading project from PHD : mira_in.phd.1
When loading strain data : mira_straindata_in.txt
When loading XML trace info files : [san]
mira_traceinfo_in.sanger.xml
[sxa]
mira_traceinfo_in.solexa.xml
When loading SSAHA2 vector screen results :
mira_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
mira_smaltvectorscreen_in.txt
When loading backbone from MAF :
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
When loading backbone from CAF :
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
When loading backbone from GenBank :
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
When loading backbone from GFF3 :
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
When loading backbone from FASTA :
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[sxa] no
Save tagged singlets in project (stsip) : [san] yes
[sxa] yes
Remove rollover tmps (rrot) : yes
Remove tmp directory (rtd) : yes
Result files:
Saved as CAF (orc) : yes
Saved as MAF (orm) : no
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : yes
Saved as GFF3 (org3) : no
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : no
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 : mira_out.caf
MAF : mira_out.maf
FASTA : mira_out.unpadded.fasta
FASTA quality : mira_out.unpadded.fasta.qual
FASTA (padded) : mira_out.padded.fasta
FASTA qual.(pad): mira_out.padded.fasta.qual
GAP4 (directory): mira_out.gap4da
ACE : mira_out.ace
HTML : mira_out.html
Simple text : mira_out.txt
TCS overview : mira_out.tcs
Wiggle : mira_out.wig
------------------------------------------------------------------------------
Deleting old directory mira_assembly ... done.
Creating directory mira_assembly ... done.
Creating directory /mnt/ngswork/tmp/mira_d_tmp ... done.
Creating directory mira_assembly/mira_d_results ... done.
Creating directory mira_assembly/mira_d_info ... done.
Creating directory mira_assembly/mira_d_chkpt ... done.
WARNING WARNING WARNING!
It looks like the tmp directory is on a NFS (Network File System) mount. This
will slow down MIRA *considerably* ... by about a factor of 10!
If you don't want that, you have three possibilities:
1) RECOMMENDED! Use -DI:trt to redirect the tmp directory somewhere else on a
local disk or even SSD.
2) POSSIBLE: put the whole project somewhere else and restart MIRA.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-MI:sonfs=no" to tell MIRA not
to stop when it finds the tmp directory on NFS.
If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.
Localtime: Fri Oct 12 14:52:33 2012
Loading backbone from FASTA file:
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat (quality:
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat.qual)
Could not find FASTA quality file
/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat.qual,
using default values for these reads.
Localtime: Fri Oct 12 14:52:33 2012
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Found 10 sequences.
Localtime: Fri Oct 12 14:52:33 2012
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 14:52:33 2012
rnm size: 0
No FASTA quality file given, using default qualities for all reads just loaded.
Localtime: Fri Oct 12 14:52:33 2012
Done.
Loaded 10 reads with 1663743 raw bases.
0 reads have quality accounted for.
Localtime: Fri Oct 12 14:52:33 2012
Generated 0 unique strain ids for 10 reads.
Postprocessing backbone(s) ... this may take a while.
10 to process
SequenceA_bb 581415
SequenceB_bb 43553
SequenceC_bb 29286
SequenceD_bb 37537
SequenceE_bb 217837
SequenceF_bb 38235
SequenceG_bb 9944
SequenceH_bb 178611
SequenceI_bb 17048
SequenceJ_bb 510277
Strain "default" has 10 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Fri Oct 12 14:52:33 2012
Counting sequences in FASTQ file: found 8000000 sequences.
Localtime: Fri Oct 12 14:52:45 2012
Solexa will load 8000000 reads.
Longest Sanger: 0
Longest 454: 0
Longest IonTor: 0
Longest PacBio: 0
Longest Solexa: 50
Longest Solid: 0
Longest overall: 50
Total reads to load: 8000000
-AL:shme is 0, automatically determining optimal value.
set -AL:shme 7
-SB:brl is 0, automatically determining optimal value.
brl: 114
-SB:bro is 0, automatically determining optimal value.
bro: 57
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
Reserving space for reads (this may take a while)
tcmalloc: large alloc 1862770688 bytes == 0xd3fa000 @
Reserved space for 8029184 reads (including backbone rails).
Adding rails to 10 contigs (this may take a while).
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceA_bb first rail: rr_####10####
SequenceA_bb last rail: rr_####10207####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceB_bb first rail: rr_####10208####
SequenceB_bb last rail: rr_####10969####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceC_bb first rail: rr_####10970####
SequenceC_bb last rail: rr_####11480####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceD_bb first rail: rr_####11481####
SequenceD_bb last rail: rr_####12136####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceE_bb first rail: rr_####12137####
SequenceE_bb last rail: rr_####15955####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceF_bb first rail: rr_####15956####
SequenceF_bb last rail: rr_####16623####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceG_bb first rail: rr_####16624####
SequenceG_bb last rail: rr_####16795####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceH_bb first rail: rr_####16796####
SequenceH_bb last rail: rr_####19926####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceI_bb first rail: rr_####19927####
SequenceI_bb last rail: rr_####20223####
Adding rails: length 114 and overlap 57
makeIntelligentConsensus() complete calc
SequenceJ_bb first rail: rr_####20224####
SequenceJ_bb last rail: rr_####29173####
Loading data (Solexa) from FASTQ files,
Localtime: Fri Oct 12 14:52:47 2012
Counting sequences in FASTQ file: found 8000000 sequences.
Localtime: Fri Oct 12 14:52:55 2012
Unusual offset of 35, guessing this file to be a Sanger-type FASTQ format.
Using calculated FASTQ quality offset: 33
Localtime: Fri Oct 12 14:52:55 2012
Loading data from FASTQ file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Loaded 8000000 reads, Localtime: Fri Oct 12 14:53:29 2012
Loaded 8000000 Solexa reads.
Total reads loaded: 8000000
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.
8029174 reads with valid data for assembly.
Localtime: Fri Oct 12 14:53:35 2012
Generated 4029174 unique template ids for 8029174 valid reads.
Localtime: Fri Oct 12 14:53:58 2012
Seeing strain 1: "ReferenceStrain"
Generated 1 unique strain ids for 8029174 reads.
Strain "default" has 8000000 reads.
Strain "ReferenceStrain" has 10 reads.
Have read pool with 8029174 reads.
===========================================================================
Pool statistics:
Backbones: 10 Backbone rails: 29164
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 8000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 8000000 0
Avg tot rlen 0 0 0 0 50 0
Avg rlen used 0 0 0 0 49 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 8000000 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:407951459 used bases in used reads: 399951459
Solid total bases:0 used bases in used reads: 0
===========================================================================
Starting Solexa known adaptor right clip ... Localtime: Fri Oct 12 14:54:11 2012
Searching multithread now ...
2
Searching for Solexa partial end adaptors ...
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done. Clipped 1447 reads.
Starting minimum quality threshold clip ... done. Killed 114482 reads.
Clipping dubious poly-base stretches at end of reads ... done.
===========================================================================
Pool statistics:
Backbones: 10 Backbone rails: 29164
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 8000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 7873742 0
Avg tot rlen 0 0 0 0 50 0
Avg rlen used 0 0 0 0 49 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 7848202 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:407951459 used bases in used reads: 393034025
Solid total bases:0 used bases in used reads: 0
===========================================================================
WARNING WARNING WARNING!
It looks like the tmp directory is on a NFS (Network File System) mount. This
will slow down MIRA *considerably* ... by about a factor of 10!
If you don't want that, you have three possibilities:
1) RECOMMENDED! Use -DI:trt to redirect the tmp directory somewhere else on a
local disk or even SSD.
2) POSSIBLE: put the whole project somewhere else and restart MIRA.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-MI:sonfs=no" to tell MIRA not
to stop when it finds the tmp directory on NFS.
If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.
Hash analysis for proposed cutbacks:Localtime: Fri Oct 12 14:56:20 2012
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Fri Oct 12 14:57:20 2012
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 14:59:52 2012
clean up temporary stat files...Localtime: Fri Oct 12 15:00:03 2012
Localtime: Fri Oct 12 15:00:09 2012
Hash statistics:
=========================================================
Measured avg. frequency coverage: 144
Deduced thresholds:
-------------------
Min normal cov: 57.6
Max normal cov: 230.4
Repeat cov: 273.6
Heavy cov: 1152
Crazy cov: 2880
Mask cov: 14400
Repeat ratio histogram:
-----------------------
0 10732442
1 1315389
2 539641
3 57738
4 20712
5 16432
6 11073
7 7202
8 4318
9 3092
10 2012
11 1122
12 762
13 544
14 454
15 422
16 294
17 321
18 378
19 264
20 210
21 220
22 210
23 182
24 126
25 100
26 102
27 74
28 92
29 24
30 12
62 2
64 4
65 4
68 2
69 2
70 2
72 2
89 2
91 2
92 2
99 2
104 2
154 2
162 4
331 2
566 2
575 2
=========================================================
Assigning statistics values:
Localtime: Fri Oct 12 15:00:09 2012
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 15:02:04 2012
Localtime: Fri Oct 12 15:02:04 2012
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 735362
Num reads cliped right: 909902
Num reads completely killed: 343151
Total bases clipped : 24823812
Clipping dubious poly-base stretches at end of reads ... done.
Hash analysis for proposed cutbacks:Localtime: Fri Oct 12 15:02:15 2012
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Fri Oct 12 15:03:03 2012
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 15:05:22 2012
clean up temporary stat files...Localtime: Fri Oct 12 15:05:33 2012
Localtime: Fri Oct 12 15:05:38 2012
Hash statistics:
=========================================================
Measured avg. frequency coverage: 150
Deduced thresholds:
-------------------
Min normal cov: 60
Max normal cov: 240
Repeat cov: 285
Heavy cov: 1200
Crazy cov: 3000
Mask cov: 15000
Repeat ratio histogram:
-----------------------
0 9239953
1 1358244
2 484851
3 47234
4 20968
5 15379
6 10700
7 6496
8 3929
9 2822
10 1600
11 1002
12 642
13 474
14 500
15 330
16 324
17 394
18 318
19 214
20 220
21 224
22 190
23 134
24 102
25 112
26 70
27 94
28 22
29 6
60 2
61 4
63 4
65 2
66 2
67 2
69 2
86 2
87 2
89 2
95 2
100 2
147 2
155 4
317 2
543 2
552 2
=========================================================
Assigning statistics values:
Localtime: Fri Oct 12 15:05:38 2012
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 15:07:26 2012
Localtime: Fri Oct 12 15:07:26 2012
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 24558
Num reads cliped right: 5330
Num reads completely killed: 9697
Total bases clipped : 206542
Clipping dubious poly-base stretches at end of reads ... done.
===========================================================================
Pool statistics:
Backbones: 10 Backbone rails: 29164
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 8000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 7510444 0
Avg tot rlen 0 0 0 0 50 0
Avg rlen used 0 0 0 0 48 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 6738806 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:407951459 used bases in used reads: 365294273
Solid total bases:0 used bases in used reads: 0
===========================================================================
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 10326
Pid: 10326
PPid: 10325
TracerPid: 0
Uid: 1001 1001 1001 1001
Gid: 1001 1001 1001 1001
FDSize: 64
Groups: 1001 65436
VmPeak: 6841808 kB
VmSize: 6840784 kB
VmLck: 0 kB
VmHWM: 6708440 kB
VmRSS: 6707208 kB
VmData: 6835424 kB
VmStk: 88 kB
VmExe: 5236 kB
VmLib: 0 kB
VmPTE: 13156 kB
Threads: 1
SigQ: 0/257903
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000001001000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 102395
nonvoluntary_ctxt_switches: 125098
--------------------------------------------------------------------------------
Pass: 1 / 2
Performing snapshot 1
Localtime: Fri Oct 12 15:07:36 2012
Localtime: Fri Oct 12 15:08:19 2012
===========================================================================
Pool statistics:
Backbones: 10 Backbone rails: 29164
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 8000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 7510444 0
Avg tot rlen 0 0 0 0 50 0
Avg rlen used 0 0 0 0 48 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 6738806 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:407951459 used bases in used reads: 365294273
Solid total bases:0 used bases in used reads: 0
===========================================================================
Localtime: Fri Oct 12 15:08:21 2012
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Fri Oct 12 15:09:19 2012
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 15:11:39 2012
clean up temporary stat files...Localtime: Fri Oct 12 15:11:50 2012
Localtime: Fri Oct 12 15:11:55 2012
Hash statistics:
=========================================================
Measured avg. frequency coverage: 151
Deduced thresholds:
-------------------
Min normal cov: 60.4
Max normal cov: 241.6
Repeat cov: 286.9
Heavy cov: 1208
Crazy cov: 3020
Mask cov: 15100
Repeat ratio histogram:
-----------------------
0 9013477
1 1364172
2 472327
3 45634
4 21020
5 15215
6 10536
7 6404
8 3835
9 2782
10 1536
11 970
12 640
13 468
14 504
15 322
16 336
17 386
18 292
19 212
20 234
21 220
22 186
23 124
24 116
25 94
26 76
27 84
28 22
59 2
61 4
62 4
65 4
67 2
68 2
85 2
86 2
88 2
95 2
100 2
146 2
154 4
315 2
539 2
548 2
=========================================================
Assigning statistics values:
Localtime: Fri Oct 12 15:11:55 2012
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Fri Oct 12 15:13:43 2012
Buntifying reads (this may take a while) ... done.
Writing read repeat info to:
mira_assembly/mira_d_info/mira_info_readrepeats.lst ... 297584 sequences with
329984 masked stretches.
Localtime: Fri Oct 12 15:13:55 2012
Searching for possible overlaps:
Localtime: Fri Oct 12 15:13:55 2012
Now running threaded and partitioned skimmer with 4 partitions in 2 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
truncating /mnt/ngswork/tmp/mira_d_tmp/mira_int_posmatchf_pass.1.bin from
9466535472 to 5867261664
truncating /mnt/ngswork/tmp/mira_d_tmp/mira_int_posmatchc_pass.1.bin from
6511158792 to 4954005408
Skim summary:
accepted: 1274677492
possible: 2511790347
permbans: 0
Hits chosen: 665737261
Localtime: Fri Oct 12 16:06:31 2012
Total megahubs: 0
Cutting back possible chimeras ... done.
Performing snapshot 0
Localtime: Fri Oct 12 16:06:44 2012
Localtime: Fri Oct 12 16:07:45 2012
Chimeras were searched for ... looking for hits to purge.
truncating /mnt/ngswork/tmp/mira_d_tmp/mira_int_posmatchf_pass.1.bin from
5867261664 to 5867134560
truncating /mnt/ngswork/tmp/mira_d_tmp/mira_int_posmatchc_pass.1.bin from
4954005408 to 4953861024
System memory: 33808089088
Mem2keepfree: 5071213363
Used by MIRA: 7761133568
Mem avail: 20975742157
rsh increased memtouse to: 20975742157
tcmalloc: large alloc 18038853632 bytes == (nil) @
tcmalloc: large alloc 18005241856 bytes == (nil) @
tcmalloc: large alloc 17971568640 bytes == (nil) @
tcmalloc: large alloc 17938063360 bytes == (nil) @
tcmalloc: large alloc 17904410624 bytes == (nil) @
tcmalloc: large alloc 17870856192 bytes == (nil) @
tcmalloc: large alloc 17837133824 bytes == (nil) @
tcmalloc: large alloc 17803640832 bytes == (nil) @
tcmalloc: large alloc 17769951232 bytes == (nil) @
tcmalloc: large alloc 17736376320 bytes == (nil) @
tcmalloc: large alloc 17702862848 bytes == (nil) @
tcmalloc: large alloc 17669242880 bytes == (nil) @
tcmalloc: large alloc 17635647488 bytes == (nil) @
tcmalloc: large alloc 17602019328 bytes == (nil) @
tcmalloc: large alloc 17568460800 bytes == (nil) @
tcmalloc: large alloc 17534865408 bytes == (nil) @
tcmalloc: large alloc 17501249536 bytes == (nil) @
tcmalloc: large alloc 17467658240 bytes == (nil) @
tcmalloc: large alloc 17434042368 bytes == (nil) @
tcmalloc: large alloc 17400422400 bytes == (nil) @
tcmalloc: large alloc 17366859776 bytes == (nil) @
tcmalloc: large alloc 17333215232 bytes == (nil) @
tcmalloc: large alloc 17299656704 bytes == (nil) @
tcmalloc: large alloc 17266053120 bytes == (nil) @
tcmalloc: large alloc 17232334848 bytes == (nil) @
tcmalloc: large alloc 17198813184 bytes == (nil) @
tcmalloc: large alloc 17165246464 bytes == (nil) @
tcmalloc: large alloc 17131663360 bytes == (nil) @
tcmalloc: large alloc 17098063872 bytes == (nil) @
tcmalloc: large alloc 17064460288 bytes == (nil) @
tcmalloc: large alloc 17030864896 bytes == (nil) @
tcmalloc: large alloc 16997216256 bytes == (nil) @
tcmalloc: large alloc 16963661824 bytes == (nil) @
tcmalloc: large alloc 16930045952 bytes == (nil) @
tcmalloc: large alloc 16896462848 bytes == (nil) @
tcmalloc: large alloc 16862806016 bytes == (nil) @
tcmalloc: large alloc 16829251584 bytes == (nil) @
tcmalloc: large alloc 16795648000 bytes == (nil) @
tcmalloc: large alloc 16762048512 bytes == (nil) @
tcmalloc: large alloc 16728461312 bytes == (nil) @
tcmalloc: large alloc 16694837248 bytes == (nil) @
tcmalloc: large alloc 16661233664 bytes == 0x1c173d000 @
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Need to reduce memory 1 ... retrying.
Can load up to 520663516 skim edges at once.
Partitioning into 2 blocks.
We have 901749632 skims in file.
Localtime: Fri Oct 12 16:10:40 2012
De-normalising SKIM hits ... (this will take a while)
Loading skims in id range 0 to 2562415
Localtime: Fri Oct 12 16:16:23 2012
Loaded 495870016 elements.
Sorting ... done.
Localtime: Fri Oct 12 16:20:12 2012
Writing normalised skimblock 0 ( 14.8 GiB) ... done.
Loading skims in id range 2562416 to 8029173
Localtime: Fri Oct 12 16:25:53 2012
Loaded 405879616 elements.
Sorting ... done.
Localtime: Fri Oct 12 16:28:57 2012
Writing normalised skimblock 2562416 ( 12.1 GiB) ... done.
Localtime: Fri Oct 12 16:29:53 2012
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Localtime: Fri Oct 12 16:32:59 2012
Step rail
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Count mappings:
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Now take maps;
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Localtime: Fri Oct 12 16:51:11 2012
Total skims taken: 5379637
Step 0
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Localtime: Fri Oct 12 16:57:41 2012
Only short reads
Step 10
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 5393501
Step 20
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 5437452
Step 30
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 5437452
Step 40
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 5437452
Step 50
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 16380170
Step 55
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 24303955
Step 56
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 24328946
Step 60
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Total skims taken: 24363031
Step solexa by critlevel
rsh4_takeSolexaByCritLevel.
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Taken 6579366 hits.
Step template overlaps
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Step NAO
rsh4_takeNeedAllOverlaps.
Loading block 0
Loading 495870016 elements at offset 0
Loaded 495870016 elements
Loading block 1
Loading 405879616 elements at offset 15867840512
Loaded 405879616 elements
Taken 0 hits.
Total skims taken: 30944173
Filtering forward skims.
Localtime: Fri Oct 12 17:38:08 2012
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Filtering complement skims.
Localtime: Fri Oct 12 17:47:44 2012
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done all filtering.
Localtime: Fri Oct 12 17:50:41 2012
Making alignments.
Localtime: Fri Oct 12 17:51:39 2012
Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 16899690
Calculated: 67407
Evaded (PB): 3
Rejected (checkfun): 0
Trans 100 saved: 16832280
Banned overlap pairs: 19294 in 5917 sets.
Localtime: Fri Oct 12 17:54:15 2012
Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 14044483
Calculated: 63923
Evaded (PB): 12
Rejected (checkfun): 0
Trans 100 saved: 13980548
Banned overlap pairs: 36304 in 8533 sets.
Localtime: Fri Oct 12 17:55:21 2012
Localtime: Fri Oct 12 17:55:22 2012
Counting number of alignments in file ... done.
Expecting 30907854 alignments.
Localtime: Fri Oct 12 17:56:02 2012
Loading confirmed overlaps from disk (will need approximately 1.7 GiB RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Found 6 banned facts.
Localtime: Fri Oct 12 17:57:36 2012
Resizing pool to 30907848 overlaps.
Sorting confirmed overlaps (this may take a while) ... done.
Localtime: Fri Oct 12 17:57:53 2012
Generating clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Sorting clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Fri Oct 12 17:58:05 2012
Writing clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing unclustered reads ... done.
Localtime: Fri Oct 12 17:58:12 2012
BFC: 1 0
overlapcompressstepping: 100000
nextoverlapcompress: 100000
Moving small clusters to debris:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done. 121167 reads moved to debris.
bfc 1
Localtime: Fri Oct 12 17:58:22 2012
Timing BFC unused: 20475
Unused: 6981510
AS_used_ids.size(): 8029174
bfc 2
Timing BFC prelim1: 13
bfc 3
bfc 4
bfc 5
Timing BFC setup AS_used_ids: 0
bfc 6/0
Timing BFC discard con: 5
bfc 7/0
Building new contig 1
Localtime: Fri Oct 12 17:58:22 2012
Unused reads: 6981510
bfc 8/0
assemblymode_mapping: 0
use genomic pathfinder: 1
Timing n4_basicCSBSSetup cleararrays: 5284
Timing n4_basicCSBSSetup init pf_banned: 505944
Timing n4_basicCSBSSetup lowerbound_oedges: 1102942
Timing n4_basicCSBSSetup total: 1614222
Timing n4_searchBestStrongGoodStartEnvironment 1 1 1 1: 687855
Startcache size: 2965
Timing n4_searchBestStrongGoodStartEnvironment sort: 114
Timing n4_searchBestStrongGoodStartEnvironment total: 688001
+[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 80 26 /
1018 / 0
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 80 77 /
1000 / 0
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 90 88 /
562 / 0
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 100
102 / 519 / 0
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 126
120 / 411 / 0
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 133
138 / 782 / 0
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[19541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6112
4 / 91 / 0
[19601] +++++++++++++++++++++++++++++++++++++++++++aa+++++++++++++++ 6112
4 / 173 / 1
[19659] ++++++++++++++++++++++a++++++++++++++++a++++++++++++++++++++ 6154
199 / 326 / 2
[19717] ++++++++++++++++++aaa+a++++++aa+a++a++++a+a+++++++++++++++++ 6382
11 / 178 / 1
[19767] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 6403
143 / 80 / 2
[19826] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 6439
185 / 211 / 6
[19885] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6496
138 / 198 / 0
[19945] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6553
5 / 397 / 0
[20005] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6610
6 / 602 / 0
[20065] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6610
4 / 1111 / 0
[20125] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6610
4 / 432 / 0
[20185] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6667
5 / 581 / 0
[20245] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6667
4 / 517 / 0
[20305] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6667
5 / 498 / 0
[20365] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6724
5 / 553 / 0
[20425] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6724
5 / 227 / 0
[20485] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6724
9 / 575 / 0
[20545] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6724
9 / 329 / 0
[20605] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6781
11 / 242 / 0
[20665] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6781
13 / 288 / 0
[20725] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6781
20 / 758 / 0
[20785] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6803
30 / 768 / 0
[20845] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6803
53 / 191 / 0
[20905] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6803
76 / 937 / 0
[20965] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6838
43 / 490 / 0
[21025] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6838
7 / 462 / 0
[21085] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6838
9 / 447 / 0
[21145] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6838
11 / 195 / 0
[21205] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6838
13 / 924 / 0
[21265] ++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++ 6895
14 / 391 / 37
[21324] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6895
14 / 532 / 0
[21384] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6895
15 / 142 / 0
[21444] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6895
17 / 544 / 0
[21504] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6895
17 / 63 / 0
[21564] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6952
12 / 273 / 0
[21624] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6952
10 / 134 / 0
[21684] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6952
13 / 168 / 0
[21744] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6952
15 / 148 / 0
[21804] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6952
17 / 311 / 0
[21864] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6952
19 / 264 / 0
[21924] ++++++++++++++++++++++++++++++++a++++++++a+a++++++++++++++++ 6952
19 / 36 / 21
[21981] +++++++++++++++++++++++a+++aaa+++aaaaa+aaaaGdTiming BFC paf construct:
11449988
bfc 9/0
Finished building.
Localtime: Fri Oct 12 17:58:34 2012
Timing BFC analysereadcov: 4221567
makeIntelligentConsensus() complete calc
-------------- Contig statistics ----------------
Contig id: 1
Contig length: 7009
Sanger 454 IonTor PacBio Solexa
Solid
Num. reads 0 0 0 0 21896
0
100% merged reads - - - - 0
0
Avg. read len 0 0 0 0 49
0
Max. coverage 2 0 0 0 364
0
Avg. coverage 0.000 0.000 0.000 0.000 155.348
0.000
Max. contig coverage: 366
Avg. contig coverage: 155.348
Consensus contains: A: 2495 C: 896 G: 1316 T: 2249 N: 0
IUPAC: 0 Funny: 52 *: 1
GC content: 31.800%
-------------------------------------------------
Timing BFC cout constats: 105376
Localtime: Fri Oct 12 17:58:38 2012
bfc 10/0
Timing BFC edit tricky1: 235
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 3 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 33704
bfc 11/0
Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 174 positions.
Deleting superfluous gap columns ... done.
Timing BFC edit single discrepancy, no HAF: 37535
bfc 12/0
Timing BFC delPSHP: 726
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering read tags to readpool.
Transfering tags to readpool.
Timing BFC crtag2rp transfer: 130889
Done.
bfc 17/0
Accepting probably misassembled contig because of too many iterations.
bfc 19
Storing contig ... 10Transforming CER mappings.
done transforming CER mappings.
Searching for: SROs UNSs IUPACs, preparing needed data: sorting tags ...
makeIntelligentConsensus() complete calc
fetching consensus for strain0 ...fetching consensus for strain1 ...(strain 1
empty.) ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 438942
Contig coverage analysis ... Timing BFC loop total: 16439042
bfc 1
Localtime: Fri Oct 12 17:58:39 2012
Timing BFC unused: 20604
Unused: 6959499
AS_used_ids.size(): 8029174
bfc 2
Timing BFC prelim1: 5
bfc 3
bfc 4
bfc 5
Timing BFC setup AS_used_ids: 1
bfc 6/0
Timing BFC discard con: 2
bfc 7/0
Building new contig 2
Localtime: Fri Oct 12 17:58:39 2012
Unused reads: 6959499
bfc 8/0
assemblymode_mapping: 0
use genomic pathfinder: 1
Timing n4_basicCSBSSetup cleararrays: 2685
Timing n4_basicCSBSSetup init pf_banned: 39
Timing n4_basicCSBSSetup total: 2727
+[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 64 23 /
562 / 0
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 80 66 /
227 / 0
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 96 77 /
444 / 0
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 111
85 / 589 / 0
[241] ++++++++++++++++++++++++++++++a+a++a+++a++++++++++++++++++++ 126
81 / 404 / 27
[297] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 161
50 / 427 / 0
[357] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 161
44 / 549 / 0
[417] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 161
46 / 612 / 0
[477] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 171
46 / 1023 / 0
[537] ++++++++++++++++++++++++++++++++++++a+a+++++++++++++++++++++ 285
30 / 401 / 49
[595] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 285
8 / 134 / 0
[655] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 285
10 / 575 / 0
[715] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 285
10 / 307 / 0
[775] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 285
12 / 718 / 0
[835] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 303
29 / 311 / 0
[895] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 330
63 / 193 / 0
[955] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 399
79 / 457 / 0
[1015] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 399
56 / 308 / 0
[1075] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 399
56 / 220 / 0
[1135] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 399
26 / 545 / 0
[1195] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 399
60 / 753 / 0
[1255] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 399
67 / 194 / 0
[1315] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
72 / 439 / 0
[1375] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
61 / 268 / 0
[1435] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
16 / 487 / 0
[1495] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
11 / 486 / 0
[1555] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
8 / 357 / 0
[1615] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
13 / 443 / 0
[1675] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
15 / 147 / 0
[1735] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
19 / 503 / 0
[1795] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
23 / 263 / 0
[1855] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
26 / 435 / 0
[1915] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 480
40 / 412 / 0
[1975] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 570
61 / 187 / 0
[2035] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 570
67 / 74 / 0
[2095] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 570
75 / 91 / 0
[2155] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 570
82 / 313 / 0
[2215] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 627
85 / 327 / 0
[2275] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 627
122 / 165 / 0
[2335] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 627
151 / 103 / 0
[2395] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 627
155 / 161 / 0
[2455] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 627
158 / 427 / 0
[2515] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 648
167 / 353 / 0
[2575] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 664
191 / 208 / 0
[2635] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 688
214 / 283 / 0
[2695] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 688
221 / 507 / 0
[2755] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 688
222 / 367 / 0
[2815] ++++++++++++++++++++++++++++++d+++++++++++++++++++++++++++++ 689
220 / 141 / 56
[2874] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 689
209 / 265 / 0
[2934] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 693
135 / 205 / 0
[2994] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 718
50 / 55 / 102
[3053] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 739
31 / 160 / 0
[3113] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 743
24 / 332 / 0
[3173] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 798
19 / 162 / 0
[3233] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 855
10 / 588 / 0
[3293] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 855
11 / 243 / 0
[3353] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 855
15 / 344 / 2
[3412] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 855
15 / 142 / 0
[3472] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 855
17 / 308 / 0
[3532] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 869
20 / 607 / 0
[3592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 969
32 / 303 / 0
[3652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 969
39 / 271 / 0
[3712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 969
40 / 345 / 0
[3772] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 1083
31 / 694 / 29
[3831] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1083
17 / 158 / 0
[3891] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1083
20 / 365 / 0
[3951] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1083
22 / 663 / 0
[4011] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1140
22 / 480 / 0
[4071] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 1140
30 / 506 / 2
[4130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1144
72 / 291 / 0
[4190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1145
95 / 483 / 0
[4250] +aaa++++++++aaaaa++++++++++++a+++aaaaaaaaaaa++++aaa+++++++++ 1145
105 / 340 / 7
[4287] aaaaa+++++++++aaaaa+++++++++aaaaaaaaaa++a+aaaaa+++++a+++aaa+ 1145
108 / 161 / 10
[4317] +a++aaa++++aaa+aaaaaaaa+aaaaaa++++++++++++++++++++++++++++++ 1145
105 / 144 / 11
[4356] ++++aa+aaaa+aaaa++++++++aaaa++++++++++++++++++++++++++++++++ 1156
125 / 199 / 17
[4402] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1188
148 / 361 / 0
[4462] ++++++++++++++++++++++++++++++++++++++++++++da++++++++++++++ 1251
176 / 396 / 13
[4520] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1251
194 / 1102 / 0
[4580] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1252
201 / 685 / 0
[4640] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1252
200 / 307 / 0
[4700] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1308
202 / 263 / 0
[4760] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1308
213 / 253 / 0
[4820] +++++++++++++++a+++aaaaaaaaa++++++++++++++++++++++++++++++++ 1308
236 / 162 / 13
[4870] ++++++++++a++++a+aaaa+++++++++++++++++++++++++++++++++++++++ 1308
233 / 175 / 18
[4924] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1313
252 / 368 / 0
[4984] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1328
281 / 533 / 0
[5044] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1354
297 / 310 / 0
[5104] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1374
324 / 123 / 0
[5164] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1383
361 / 468 / 0
[5224] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1401
379 / 754 / 0
[5284] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1405
408 / 662 / 0
[5344] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1422
412 / 166 / 0
[5404] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1426
441 / 394 / 0
[5464] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1441
457 / 307 / 0
[5524] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1456
458 / 333 / 0
[5584] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1473
471 / 218 / 0
[5644] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1482
490 / 355 / 0
[5704] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1506
509 / 249 / 0
[5764] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1517
541 / 355 / 0
[5824] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1519
547 / 222 / 0
[5884] +++++++++++++++++++d++++++++++++++++++++++++++++++++++++++++ 1562
550 / 643 / 301
[5943] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1569
561 / 23 / 0
[6003] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 1626
573 / 177 / 1
[6062] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1626
590 / 429 / 0
[6122] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1626
599 / 165 / 0
[6182] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1628
633 / 76 / 0
[6242] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1630
661 / 23 / 0
[6302] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1653
659 / 705 / 0
[6362] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1667
671 / 484 / 0
[6422] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1683
644 / 377 / 0
[6482] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1683
599 / 335 / 0
[6542] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1683
538 / 140 / 0
[6602] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1683
565 / 66 / 0
[6662] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1683
566 / 134 / 0
[6722] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1740
545 / 276 / 0
[6782] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1742
524 / 313 / 0
[6842] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1742
525 / 301 / 0
[6902] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1742
529 / 154 / 0
[6962] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1817
533 / 211 / 0
[7022] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1817
559 / 150 / 0
[7082] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1822
600 / 429 / 0
[7142] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1836
648 / 492 / 0
[7202] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1841
668 / 513 / 0
[7262] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1874
667 / 303 / 0
[7322] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1879
684 / 471 / 0
[7382] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1894
711 / 439 / 0
[7442] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1905
707 / 146 / 0
[7502] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1924
721 / 109 / 0
[7562] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1924
716 / 155 / 0
[7622] ++++++++++++++++a++++++++++++++++++++++++++a++++++++++++++++ 1988
699 / 345 / 2
[7680] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1988
683 / 365 / 0
[7740] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1988
684 / 176 / 0
[7800] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1988
649 / 288 / 0
[7860] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1988
658 / 356 / 0
[7920] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2045
666 / 162 / 0
[7980] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2045
650 / 398 / 0
[8040] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2045
681 / 730 / 0
[8100] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2045
700 / 145 / 0
[8160] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2045
732 / 280 / 0
[8220] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 2116
750 / 248 / 20
[8279] +++++++++++++++++++++++++++++++++a++++++++++a++a+aaa+a++aaaa 2121
782 / 371 / 11
[8328] aa+aaaaaa+++aaaaaa+++++++++++++++++aaaaaa+aaaaaa++++++++aaa+ 2121
803 / 126 / 13
[8359] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2121
801 / 106 / 0
[8419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2121
810 / 167 / 0
[8479] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2178
794 / 365 / 0
[8539] ++++++++++++++++aaaa+++++++++++++++++++++++++++++++aaaaaaaaa 2178
739 / 128 / 16
[8586] ++++++++++++++++++++++++aaaaaaaaaaaaa+aaaaaaaaaaaaaa++aaaaaa 2178
689 / 139 / 17
[8613] +a+a+a+a++++a+aaaa++++++++++++a++++++a++++++++++++++++++++++ 2178
657 / 459 / 19
[8662] ++++++++++++a+a+a+aa+++++++aaa+++++aaa+++a+aaaaaaa++++++++++ 2178
680 / 80 / 31
[8703] ++++++++++++++++++++++++++++++aaa+a+a+aaaaa++aaa++++++++++++ 2178
689 / 303 / 40
[8750] +++++++++++++aaaaaa+++++++++++++++++a+++a+aaaaa+++aaaaaaaaaa 2178
702 / 595 / 42
[8787] +++++++++aaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaaaaaaaaaaaaaaaaa++a 2178
699 / 458 / 41
[8799] ++aaaa+++a+++++++++a++a+++++++++++++++aaaaaaaaaaaaaaaaaaaaaa 2178
666 / 257 / 47
[8830] aaaaa+++aa+aa+++++aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa++aaaaaaaa 2178
660 / 322 / 41
[8841] aaaaaaaaaaaaaa++a+++++++++++++++++++++++++++++++++++++++++++ 2192
629 / 176 / 23
[8886] ++++++++++++++++++++++++++++++++d++++aaaa+++++++++a+++++++++ 2274
620 / 375 / 29
[8940] +++++++aaaaaa++a+++++++++++++++++++++++++a++++++++++++++++++ 2274
541 / 253 / 26
[8992] +++++++++a++++++++++a+aaaaaaaaaaaaaaaaaaaaaaa+++++++++++++++ 2274
453 / 162 / 21
[9027] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2295
485 / 483 / 0
[9087] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2319
532 / 403 / 0
[9147] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2321
558 / 448 / 0
[9207] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2321
563 / 425 / 0
[9267] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2331
568 / 204 / 0
[9327] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2331
578 / 346 / 0
[9387] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2343
586 / 158 / 0
[9447] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2343
596 / 144 / 0
[9507] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
562 / 218 / 0
[9567] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
447 / 645 / 0
[9627] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
296 / 561 / 0
[9687] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
182 / 62 / 0
[9747] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
125 / 27 / 127
[9806] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
30 / 82 / 145
[9865] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
16 / 199 / 0
[9925] ++++++++++++aaaaa+++++++++++++++++++++++++++++++++++++++++++ 2388
18 / 316 / 57
[9980] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
22 / 275 / 0
[10040] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2388
27 / 259 / 0
[10100] +++++++++++++++++++++++d++++++++++++++++++++++++++++++++++++ 2445
39 / 272 / 78
[10159] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2445
59 / 337 / 0
[10219] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2445
70 / 385 / 0
[10279] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2445
76 / 222 / 0
[10339] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2445
77 / 160 / 0
[10399] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2445
78 / 23 / 0
[10459] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2450
81 / 208 / 0
[10519] ++++++++++++++++++++++++++++++++++++++++a+a+++++++++++++++++ 2467
90 / 155 / 152
[10577] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 2467
91 / 202 / 46
[10636] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2477
51 / 97 / 0
[10696] ++++++++++++++++++++++++++++++++++++++++d+++++++++++++++++++ 2517
47 / 26 / 135
[10755] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2560
76 / 155 / 0
[10815] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2564
97 / 61 / 0
[10875] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
85 / 152 / 0
[10935] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
35 / 394 / 0
[10995] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
27 / 110 / 0
[11055] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
29 / 239 / 0
[11115] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
33 / 287 / 0
[11175] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
34 / 22 / 0
[11235] ++++++++++++++++++++++++++++++++++++++++++++++++++++d+++++++ 2616
38 / 365 / 184
[11294] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
31 / 234 / 0
[11354] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2616
35 / 130 / 0
[11414] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2680
38 / 257 / 0
[11474] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2696
61 / 168 / 0
[11534] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2722
74 / 375 / 0
[11594] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2749
75 / 394 / 0
[11654] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2777
80 / 717 / 0
[11714] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2814
92 / 330 / 0
[11774] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2834
110 / 265 / 0
[11834] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2864
149 / 795 / 0
[11894] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2868
164 / 450 / 0
[11954] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2888
179 / 506 / 0
[12014] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2900
189 / 512 / 0
[12074] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2912
202 / 532 / 0
[12134] +++++++++++++++++++++++++++++++++++++++++++++++++++++++d++++ 2957
194 / 507 / 152
[12193] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2962
215 / 323 / 0
[12253] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2977
246 / 173 / 0
[12313] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 2989
275 / 172 / 38
[12372] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3001
293 / 691 / 0
[12432] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3017
317 / 249 / 0
[12492] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3028
346 / 239 / 0
[12552] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3036
352 / 524 / 0
[12612] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3061
355 / 77 / 0
[12672] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3085
384 / 21 / 0
[12732] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
404 / 21 / 0
[12792] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
425 / 920 / 0
[12852] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 3121
408 / 335 / 35
[12911] ++++++++++++++++++++++++++d+++++++++++++++++++++++++++++++++ 3121
365 / 142 / 186
[12970] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
272 / 667 / 0
[13030] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
203 / 158 / 0
[13090] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
192 / 460 / 0
[13150] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
193 / 220 / 0
[13210] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
195 / 60 / 0
[13270] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3121
197 / 320 / 0
[13330] +++++++++++++++++++++++++++++++++++++++++++d+++d++++++++++++ 3178
197 / 352 / 213
[13388] ++++++++++++++++++++++++++++++a++d++++++++++++++++++++++++++ 3178
132 / 646 / 227
[13446] +++a+++++++++d++++++++++++++++++++++++++++++++++++++++++++++ 3178
44 / 535 / 91
[13504] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3178
42 / 334 / 0
[13564] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3178
44 / 506 / 0
[13624] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3178
47 / 475 / 0
[13684] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3178
48 / 485 / 0
[13744] ++++++++++++++++++++++++++++d++++++++++++++++a++++++++++++++ 3235
45 / 435 / 174
[13802] +++++++d++d+a+++++++++++++++++++++++++++++++++++++++++++++++ 3235
28 / 360 / 175
[13859] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3235
26 / 167 / 0
[13919] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3235
28 / 386 / 0
[13979] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3235
29 / 311 / 0
[14039] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3235
30 / 78 / 0
[14099] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 3292
24 / 127 / 2
[14158] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3292
24 / 505 / 0
[14218] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3292
25 / 115 / 0
[14278] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3292
27 / 288 / 0
[14338] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3292
27 / 22 / 0
[14398] +++++++++++++++++++++++++++++++a++a+++++++++++++++++++++++++ 3349
25 / 405 / 1
[14456] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3349
24 / 308 / 0
[14516] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3349
30 / 53 / 0
[14576] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3349
40 / 548 / 0
[14636] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3361
55 / 83 / 0
[14696] +++++++++++++++++++++++++++++++++++++++++++++++a++++++++++++ 3406
85 / 247 / 115
[14755] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3406
92 / 125 / 0
[14815] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3406
83 / 385 / 0
[14875] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3406
29 / 330 / 0
[14935] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3406
16 / 410 / 0
[14995] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3406
18 / 200 / 0
[15055] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
16 / 140 / 0
[15115] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
14 / 414 / 0
[15175] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
15 / 278 / 0
[15235] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
14 / 116 / 0
[15295] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
14 / 290 / 0
[15355] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
15 / 194 / 0
[15415] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
16 / 490 / 0
[15475] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3463
16 / 355 / 0
[15535] +++++++++++++++++++++++++++++++++++++++aa+a+++++++++++++++++ 3520
16 / 361 / 32
[15592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3520
15 / 463 / 0
[15652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3520
15 / 253 / 0
[15712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3520
18 / 562 / 0
[15772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3520
19 / 450 / 0
[15832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3520
20 / 511 / 0
[15892] +++++++++++++a+++++++a++++++++++++++++++++++++++++++++++++++ 3577
12 / 431 / 2
[15950] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3577
8 / 191 / 0
[16010] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3577
10 / 382 / 0
[16070] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3577
13 / 446 / 0
[16130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3599
20 / 184 / 0
[16190] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3613
43 / 26 / 1
[16249] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3623
51 / 320 / 0
[16309] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3633
68 / 178 / 0
[16369] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3657
43 / 201 / 0
[16429] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3657
14 / 223 / 0
[16489] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3657
15 / 375 / 0
[16549] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3691
13 / 256 / 0
[16609] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3691
7 / 287 / 0
[16669] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3691
9 / 495 / 0
[16729] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3691
10 / 255 / 0
[16789] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3691
12 / 678 / 0
[16849] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3713
12 / 230 / 0
[16909] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3723
40 / 139 / 0
[16969] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3740
65 / 105 / 0
[17029] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3751
80 / 126 / 0
[17089] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3805
32 / 263 / 0
[17149] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3805
18 / 328 / 0
[17209] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3805
19 / 174 / 0
[17269] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3805
22 / 317 / 0
[17329] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3862
24 / 380 / 0
[17389] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3862
52 / 457 / 0
[17449] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3862
71 / 112 / 0
[17509] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3919
76 / 382 / 0
[17569] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3919
80 / 205 / 0
[17629] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3919
87 / 376 / 0
[17689] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3919
94 / 516 / 0
[17749] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3931
104 / 350 / 0
[17809] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3935
122 / 172 / 0
[17869] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3935
120 / 203 / 0
[17929] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 3959
99 / 541 / 8
[17988] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3959
95 / 23 / 0
[18048] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3976
92 / 548 / 0
[18108] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3976
85 / 145 / 0
[18168] +++++++++++a++++++++++++++++++++++++++++++++++++++++++++++++ 3976
68 / 470 / 105
[18227] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3976
18 / 440 / 0
[18287] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3976
14 / 358 / 0
[18347] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3976
14 / 263 / 0
[18407] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4033
15 / 249 / 0
[18467] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4033
13 / 227 / 0
[18527] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4033
14 / 59 / 0
[18587] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4033
13 / 52 / 0
[18647] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4033
14 / 373 / 0
[18707] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4033
15 / 279 / 0
[18767] ++++++++++++++++++++++++++++a+++++++a+++++++++++++++++++++++ 4090
13 / 382 / 1
[18825] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4090
7 / 285 / 0
[18885] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4090
9 / 336 / 0
[18945] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4090
12 / 579 / 0
[19005] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4090
12 / 290 / 0
[19065] ++++++++++++++++++++++++++++++++++++++++++++++++++a+a+++++++ 4147
13 / 234 / 1
[19123] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4147
10 / 22 / 0
[19183] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4147
12 / 204 / 0
[19243] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4147
14 / 128 / 0
[19303] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4147
15 / 83 / 0
[19363] +++++++++++++daaaaaaa+++++++++++++++++++++++++++++++++++++++ 4148
25 / 35 / 34
[19415] ++++++++++++++++aa++++++++++++++++++++++++++++++++++++++++++ 4148
27 / 78 / 1
[19473] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4148
93 / 145 / 0
[19533] +++++++++++a++a++a+++++++++++a+++aaaaa+a++++a++++++d+aaa++a+ 4148
632 / 56 / 28
[19577] +d++++++a+++++aaa+++a+aaaGGG++++++++daTiming BFC paf construct: 10645659
bfc 9/0
Finished building.
Localtime: Fri Oct 12 17:58:50 2012
Timing BFC analysereadcov: 535387
makeIntelligentConsensus() complete calc
-------------- Contig statistics ----------------
Contig id: 2
Contig length: 4148
Sanger 454 IonTor PacBio Solexa
Solid
Num. reads 0 0 0 0 19538
0
100% merged reads - - - - 0
0
Avg. read len 0 0 0 0 49
0
Max. coverage 2 0 0 0 369
0
Avg. coverage 0.000 0.000 0.000 0.000 234.467
0.000
Max. contig coverage: 371
Avg. contig coverage: 234.467
Consensus contains: A: 1327 C: 810 G: 556 T: 1443 N: 0
IUPAC: 1 Funny: 0 *: 11
GC content: 33.027%
-------------------------------------------------
Timing BFC cout constats: 85704
Localtime: Fri Oct 12 17:58:50 2012
bfc 10/0
Timing BFC edit tricky1: 193
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 2 new Strong RMB (SRMc)
- 2 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 32761
bfc 11/0
Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 142 positions.
Deleting superfluous gap columns ... done.
Timing BFC edit single discrepancy, no HAF: 32719
bfc 12/0
Timing BFC delPSHP: 598
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering read tags to readpool.
Transfering tags to readpool.
General error while transfering tag 2 to readpool read from:
Name: rr_####22019####
ql: 0 qr: 115
sl: 0 sr: 115
cl: 0 cr: 115
ml: 0 mr: 115
Leftclip: 0 Rightclip: 115 Len: 115 (115) LenSeq: 115
Leftextend: 0 Rightextend: 0
Template end: N Template: Int. Tname: rr_####22019####
T-ID: 22019 TPartner-ID: -1
Strain: ReferenceStrain S-ID: 0
Seqtype: san
IsBB: 0 IsRail: 1 IsCER: 0
Tags:
Tag 0: HAF3 0 56 ""
Tag 1: HAF2 57 114 ""
Tag 2: WRMr 105 107 ""
Tag 3: WRMr 107 108 ""
Read size padded: 115
Read padded sequence:
tgagatagactaaaaattaaacgctactccagcttctgcaccaatagtactgtaaaaaactttgtgtgcgcctttatcagtaacctttttctctagatcatcagga*tgtgcagg
Complement padded dirty.
Read padded sequence, adjustment, quality, baseflags:
0: t 0 30 f: valid slp fr mst #3 r; invld #0
1: g 1 30 f: valid slp fr mst #3 r; invld #0
2: a 2 30 f: valid slp fr mst #3 r; invld #0
3: g 3 30 f: valid slp fr mst #3 r; invld #0
4: a 4 30 f: valid slp fr mst #3 r; invld #0
5: t 5 30 f: valid slp fr mst #3 r; invld #0
6: a 6 30 f: valid slp fr mst #3 r; invld #0
7: g 7 30 f: valid slp fr mst #3 r; invld #0
8: a 8 30 f: valid slp fr mst #3 r; invld #0
9: c 9 30 f: valid slp fr mst #3 r; invld #0
10: t 10 30 f: valid slp fr mst #3 r; invld #0
11: a 11 30 f: valid slp fr mst #3 r; invld #0
12: a 12 30 f: valid slp fr mst #3 r; invld #0
13: a 13 30 f: valid slp fr mst #3 r; invld #0
14: a 14 30 f: valid slp fr mst #3 r; invld #0
15: a 15 30 f: valid slp fr mst #3 r; invld #0
16: t 16 30 f: valid slp fr mst #3 r; valid slp fr mst #3
17: t 17 30 f: valid slp fr mst #3 r; valid slp fr mst #3
18: a 18 30 f: valid slp fr mst #3 r; valid slp fr mst #3
19: a 19 30 f: valid slp fr mst #3 r; valid slp fr mst #3
20: a 20 30 f: valid slp fr mst #3 r; valid slp fr mst #3
21: c 21 30 f: valid slp fr mst #3 r; valid slp fr mst #3
22: g 22 30 f: valid slp fr mst #3 r; valid slp fr mst #3
23: c 23 30 f: valid slp fr mst #3 r; valid slp fr mst #3
24: t 24 30 f: valid slp fr mst #3 r; valid slp fr mst #3
25: a 25 30 f: valid slp fr mst #3 r; valid slp fr mst #3
26: c 26 30 f: valid slp fr mst #3 r; valid slp fr mst #3
27: t 27 30 f: valid slp fr mst #3 r; valid slp fr mst #3
28: c 28 30 f: valid slp fr mst #3 r; valid slp fr mst #3
29: c 29 30 f: valid slp fr mst #3 r; valid slp fr mst #3
30: a 30 30 f: valid slp fr mst #3 r; valid slp fr mst #3
31: g 31 30 f: valid slp fr mst #3 r; valid slp fr mst #3
32: c 32 30 f: valid slp fr mst #3 r; valid slp fr mst #3
33: t 33 30 f: valid slp fr mst #3 r; valid slp fr mst #3
34: t 34 30 f: valid slp fr mst #3 r; valid slp fr mst #3
35: c 35 30 f: valid slp fr mst #3 r; valid slp fr mst #3
36: t 36 30 f: valid slp fr mst #3 r; valid slp fr mst #3
37: g 37 30 f: valid slp fr mst #3 r; valid slp fr mst #3
38: c 38 30 f: valid slp fr mst #3 r; valid slp fr mst #3
39: a 39 30 f: valid slp fr mst #3 r; valid slp fr mst #3
40: c 40 30 f: valid slp fr mst #3 r; valid slp fr mst #3
41: c 41 30 f: invld #0 r; valid slp fr mst #3
42: a 42 30 f: invld #0 r; valid slp fr mst #3
43: a 43 30 f: invld #0 r; valid slp fr mst #3
44: t 44 30 f: invld #0 r; valid slp fr mst #3
45: a 45 30 f: invld #0 r; valid slp fr mst #3
46: g 46 30 f: invld #0 r; valid slp fr mst #3
47: t 47 30 f: invld #0 r; valid slp fr mst #3
48: a 48 30 f: invld #0 r; valid slp fr mst #3
49: c 49 30 f: invld #0 r; valid slp fr mst #3
50: t 50 30 f: invld #0 r; valid slp fr mst #3
51: g 51 30 f: invld #0 r; valid slp fr mst #3
52: t 52 30 f: invld #0 r; valid slp fr mst #3
53: a 53 30 f: invld #0 r; valid slp fr mst #3
54: a 54 30 f: invld #0 r; valid slp fr mst #3
55: a 55 30 f: invld #0 r; valid slp fr mst #3
56: a 56 30 f: invld #0 r; valid slp fr mst #3
57: a 57 30 f: valid slp #2 r; invld #0
58: a 58 30 f: valid slp #2 r; invld #0
59: c 59 30 f: valid slp #2 r; invld #0
60: t 60 30 f: valid slp #2 r; invld #0
61: t 61 30 f: valid slp #2 r; invld #0
62: t 62 30 f: valid #2 r; invld #0
63: g 63 30 f: valid #2 r; invld #0
64: t 64 30 f: valid #2 r; invld #0
65: g 65 30 f: valid #2 r; invld #0
66: t 66 30 f: valid #2 r; invld #0
67: g 67 30 f: valid #2 r; invld #0
68: c 68 30 f: valid #2 r; invld #0
69: g 69 30 f: valid #2 r; invld #0
70: c 70 30 f: valid #2 r; invld #0
71: c 71 30 f: valid #2 r; invld #0
72: t 72 30 f: valid #2 r; invld #0
73: t 73 30 f: valid #2 r; valid slp #2
74: t 74 30 f: valid #2 r; valid slp #2
75: a 75 30 f: valid #2 r; valid slp #2
76: t 76 30 f: valid #2 r; valid slp #2
77: c 77 30 f: valid #2 r; valid slp #2
78: a 78 30 f: valid #2 r; valid #2
79: g 79 30 f: valid #2 r; valid #2
80: t 80 30 f: valid #2 r; valid #2
81: a 81 30 f: valid #2 r; valid #2
82: a 82 30 f: valid #2 r; valid #2
83: c 83 30 f: valid #2 r; valid #2
84: c 84 30 f: valid #2 r; valid #2
85: t 85 30 f: valid #2 r; valid #2
86: t 86 30 f: valid #2 r; valid #2
87: t 87 30 f: valid #2 r; valid #2
88: t 88 30 f: valid #2 r; valid #2
89: t 89 30 f: valid #2 r; valid #2
90: c 90 30 f: valid #2 r; valid #2
91: t 91 30 f: valid #2 r; valid #2
92: c 92 30 f: valid #2 r; valid #2
93: t 93 30 f: valid #2 r; valid #2
94: a 94 30 f: valid #2 r; valid #2
95: g 95 30 f: valid #2 r; valid #2
96: a 96 30 f: valid #2 r; valid #2
97: t 97 30 f: valid #2 r; valid #2
98: c 98 30 f: invld #0 r; valid #2
99: a 99 30 f: invld #0 r; valid #2
100: t 100 30 f: invld #0 r; valid #2
101: c 101 30 f: invld #0 r; valid #2
102: a 102 30 f: invld #0 r; valid #2
103: g 103 30 f: invld #0 r; valid #2
104: g 104 30 f: invld #0 r; valid #2
105: a 105 30 f: invld #0 r; valid #2
106: * -1 30 f: invld #0 r; invld #0
107: t 106 30 f: invld #0 r; valid #2
108: g 107 30 f: invld #0 r; valid #2
109: t 108 30 f: invld #0 r; valid #2
110: g 109 30 f: invld #0 r; valid #2
111: c 110 30 f: invld #0 r; valid #2
112: a 111 30 f: invld #0 r; valid #2
113: g 112 30 f: invld #0 r; valid #2
114: g 113 30 f: invld #0 r; valid #2
Exiting.
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"id of read not found in contig?"
->Thrown: int32 Contig::getReadWithID(int32 readid) const
->Caught: void Assembly::transferContigReadTagsToReadpool(const Contig & con,
const list<Contig>::const_iterator bbContigI)
Aborting process, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/apps/trac/mira-assembler/
and also give a short notice on the mira talk mailing list.
If reporting, please do not delete the log and checkpoint directories, there may
be files in them which could be needed to find the problem.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /mnt/ngswork/galaxy/galaxy-dist/database/job_working_directory/019/19171
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
MIRA took 186.37 minutes
Return error code 1 from command:
mira --job=denovo,genome,draft -SB:lb=1:bft=fasta
-FN:bbin=/mnt/ngswork/galaxy/galaxy-dist/database/files/024/dataset_24256.dat
SOLEXA_SETTINGS -LR:lsd=1:ft=fastq
-FN:fqi=/mnt/ngswork/galaxy/galaxy-dist/database/files/023/dataset_23893.dat
-CO:msr=0 -GE:uti=0:tismin=-1:tismax=-1 COMMON_SETTINGS -MI:somrnl=0
-DI:trt=/mnt/ngswork/tmp -MI:sonfs=no
-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1
--
Brad Langhorst
langhorst@xxxxxxx<mailto:langhorst@xxxxxxx>
Other related posts:
- » [mira_talk] internal logic… error - Langhorst, Brad
