[mira_talk] Need suggestion on quality of NGS data and post assembly procedures

• From: Rameez Mj <rameez03online@xxxxxxxxx>
• To: mira_talk@xxxxxxxxxxxxx
• Date: Tue, 16 Jun 2015 14:06:06 +0530

I have a bacterial whole genome project going on with iontorrent proton
200bp platform. I analysed my data with princeq. It being of high average
coverage suggested by MIRA(129x). I removed exact duplicates with
princess-lite and extracted 1800000 reads randomly using a python script
"subsampler". MIRA assembles it to >3000 contigs (details are there in the
assembly log).Result of data analysis using princess, Assembly log and
result info generated by MIRA is attached.

Now I need any experienced person to suggest kindly that is it wise to
continue with this data? How hard it will be for me to complete this
project successfully. what are the best tools and methods I can use on
this?

I know the question is raw but I expect something from you.Thanking you in
advance.
Localtime: Mon Jun 15 19:40:54 2015

Assembly information:
=====================

Localtime: Mon Jun 15 19:40:54 2015
MIRA version: 4.0.2

Num. reads assembled: 1691299
Num. singlets: 0


Coverage assessment (calculated from contigs >= 5000 with coverage >= 26):
=========================================================
Avg. total coverage: 88.86
Avg. coverage per sequencing technology
Sanger: 0.00
454: 0.00
IonTor: 88.86
PcBioHQ: 0.00
PcBioLQ: 0.00
Text: 0.00
Solexa: 0.00
Solid: 0.00


Large contigs (makes less sense for EST assemblies):
====================================================
With Contig size >= 500
AND (Total avg. Cov >= 44
OR Cov(san) >= 0
OR Cov(454) >= 0
OR Cov(ion) >= 44
OR Cov(pbh) >= 0
OR Cov(pbl) >= 0
OR Cov(txt) >= 0
OR Cov(sxa) >= 0
OR Cov(sid) >= 0
)

Length assessment:
------------------
Number of contigs: 1350
Total consensus: 3001373
Largest contig: 22647
N50 contig size: 2952
N90 contig size: 1082
N95 contig size: 803

Coverage assessment:
--------------------
Max coverage (total): 813
Max coverage per sequencing technology
Sanger: 0
454: 0
IonTor: 813
PcBioHQ: 0
PcBioLQ: 0
Text: 0
Solexa: 0
Solid: 0

Quality assessment:
-------------------
Average consensus quality: 60
Consensus bases with IUPAC: 63 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)


All contigs:
============
Length assessment:
------------------
Number of contigs: 3400
Total consensus: 3793282
Largest contig: 22647
N50 contig size: 2355
N90 contig size: 390
N95 contig size: 275

Coverage assessment:
--------------------
Max coverage (total): 813
Max coverage per sequencing technology
Sanger: 0
454: 0
IonTor: 813
PcBioHQ: 0
PcBioLQ: 0
Text: 0
Solexa: 0
Solid: 0

Quality assessment:
-------------------
Average consensus quality: 57
Consensus bases with IUPAC: 129 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)

Attachment: PRINSEQ analysis result.pdf
Description: Adobe PDF document

This is MIRA 4.0.2 .

Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.

To (un-)subscribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html

After subscribing, mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx


To report bugs or ask for features, please use the SourceForge ticketing
system at:
http://sourceforge.net/p/mira-assembler/tickets/
This ensures that requests do not get lost.


Compiled by: bach
Fri Apr 18 14:57:20 CEST 2014
On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012
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 lab445-T1700 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10
19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Looking for files named in data ...Pushing back filename:
"/home/user/Desktop/SST/random.fastq"
Manifest:
projectname: SSTrandom
job: genome,denovo,accurate
parameters: -GE:not=4
Manifest load entries: 1
MLE 1:
RGID: 1
RGN: SSTiontorrent SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 2 (IonTor) namschem: 4 SID: 0
DQ: 20
BB: 0 Rail: 0 CER: 0

/home/user/Desktop/SST/random.fastq

Parameters parsed without error, perfect.

-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data

Used parameter settings:
General (-GE):
Project name : SSTrandom
Number of threads (not) : 4
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Colour reads by hash frequency (crhf) : yes

Load reads options (-LR):
Wants quality file (wqf) : [ion] 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
Maximum contigs per pass (mcpp) : 0

Minimum read length (mrl) : [ion] 40
Minimum reads per contig (mrpc) : [ion] 5
Enforce presence of qualities (epoq) : [ion] yes

Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [ion] 2
Minimum length (ardml) : [ion] 200
Grace length (ardgl) : [ion] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [ion] 1.5

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):
Bootstrap new backbone (bnb) : yes
Start backbone usage in pass (sbuip) : 3
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Trim overhanging reads (tor) : yes

(Also build new contigs (abnc)) : yes

Dataprocessing options (-DP):
Use read extensions (ure) : [ion] no
Read extension window length (rewl) : [ion] 15
Read extension w. maxerrors (rewme) : [ion] 2
First extension in pass (feip) : [ion] 0
Last extension in pass (leip) : [ion] 0

Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [ion] 8
Max front gap (msvsmfg) : [ion] 8
Max end gap (msvsmeg) : [ion] 12
Strict front clip (msvssfc) : [ion] 0
Strict end clip (msvssec) : [ion] 0
Possible vector leftover clip (pvlc) : [ion] no
maximum len allowed (pvcmla) : [ion] 18
Min qual. threshold for entire read (mqtfer): [ion] 0
Number of bases (mqtfernob) : [ion] 0
Quality clip (qc) : [ion] no
Minimum quality (qcmq) : [ion] 20
Window length (qcwl) : [ion] 30
Bad stretch quality clip (bsqc) : [ion] no
Minimum quality (bsqcmq) : [ion] 5
Window length (bsqcwl) : [ion] 20
Masked bases clip (mbc) : [ion] yes
Gap size (mbcgs) : [ion] 5
Max front gap (mbcmfg) : [ion] 12
Max end gap (mbcmeg) : [ion] 12
Lower case clip front (lccf) : [ion] yes
Lower case clip back (lccb) : [ion] yes
Clip poly A/T at ends (cpat) : [ion] no
Keep poly-a signal (cpkps) : [ion] no
Minimum signal length (cpmsl) : [ion] 12
Max errors allowed (cpmea) : [ion] 1
Max gap from ends (cpmgfe) : [ion] 9
Clip 3 prime polybase (c3pp) : [ion] no
Minimum signal length (c3ppmsl) : [ion] 15
Max errors allowed (c3ppmea) : [ion] 3
Max gap from ends (c3ppmgfe) : [ion] 9
Clip known adaptors right (ckar) : [ion] yes
Ensure minimum left clip (emlc) : [ion] no
Minimum left clip req. (mlcr) : [ion] 4
Set minimum left clip to (smlc) : [ion] 4
Ensure minimum right clip (emrc) : [ion] no
Minimum right clip req. (mrcr) : [ion] 10
Set minimum right clip to (smrc) : [ion] 15

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

Propose end clips (pec) : [ion] yes
Bases per hash (pecbph) : 27
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [ion] 1
Back freq (pbfreq) : [ion] 1
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [ion] no
Back forward-rev (pbfore) : [ion] no
Front conf. multi-seq type (pfcmst) : [ion] no
Back conf. multi-seq type (pbcmst) : [ion] no
Front seen at low pos (pfsalp) : [ion] no
Back seen at low pos (pbsalp) : [ion] no

Clip bad solexa ends (cbse) : [ion] no
Search PhiX174 (spx174) : [ion] no
Filter PhiX174 (fpx174) : [ion] no

Rare kmer mask (rkm) : [ion] 0

Parameters for SKIM algorithm (-SK):
Number of threads (not) : 4

Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 19
Automatic increase per pass (bphaipp) : 1
Automatic incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 1
Percent required (pr) : [ion] 50

Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0

SW check on backbones (swcob) : no

Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048

Parameters for Hash Statistics (-HS):
Freq. cov. estim. min (fcem) : 0
Freq. estim. min normal (fenn) : 0.4
Freq. estim. max normal (fexn) : 1.6
Freq. estim. repeat (fer) : 1.9
Freq. estim. heavy repeat (fehr) : 8
Freq. estim. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Nasty repeat coverage (nrc) : 0
Lossless digital normalisation (ldn) : no

Repeat level in info file (rliif) : 6

Million hashes per buffer (mhpb) : 16
Rare kmer early kill (rkek) : no

Pathfinder options (-PF):
Use quick rule (uqr) : [ion] yes
Quick rule min len 1 (qrml1) : [ion] 80
Quick rule min sim 1 (qrms1) : [ion] 90
Quick rule min len 2 (qrml2) : [ion] 60
Quick rule min sim 2 (qrms2) : [ion] 95
Backbone quick overlap min len (bqoml) : [ion] 80
Max. start cache fill time (mscft) : 5

Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [ion] 20
Bandwidth max (bmax) : [ion] 80
Bandwidth min (bmin) : [ion] 20
Minimum score (ms) : [ion] 15
Minimum overlap (mo) : [ion] 19
Minimum relative score in % (mrs) : [ion] 70
Solexa_hack_max_errors (shme) : [ion] -1
Extra gap penalty (egp) : [ion] yes
extra gap penalty level (egpl) : [ion] reject_codongaps
Max. egp in percent (megpp) : [ion] 100

Contig parameters (-CO):
Name prefix (np) : SSTrandom
Reject on drop in relative alignment score in % (rodirs) : [ion] 25
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [ion] 4
Minimum neighbour quality needed for tagging (mnq) : [ion] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [ion] 25
End-read Marking Exclusion Area in bases (emea) : [ion] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [ion] no
Also mark gap bases - even multicolumn (amgbemc) : [ion] yes
Also mark gap bases - need both strands (amgbnbs): [ion] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [ion] no
Merge short reads (msr) : [ion] no
Max errors (msrme) : [ion] 0
Keep ends unmerged (msrkeu) : [ion] -1
Gap override ratio (gor) : [ion] 66

Edit options (-ED):
Mira automatic contig editing (mace) : yes
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [ion] yes

Misc (-MI):
Large contig size (lcs) : 500
Large contig size for stats (lcs4s) : 5000

I know what I do (ikwid) : no

Extra flag 1 / sanity track check (ef1) : no
Extra flag 2 / dnredreadsatpeaks (ef2) : yes
Extra flag 3 / pelibdisassemble (ef3) : yes
Extended log (el) : no

Nag and Warn (-NW):
Check NFS (cnfs) : stop
Check multi pass mapping (cmpm) : stop
Check template problems (ctp) : stop
Check duplicate read names (cdrn) : stop
Check max read name length (cmrnl) : stop
Max read name length (mrnl) : 40
Check average coverage (cac) : stop
Average coverage value (acv) : 80

Directories (-DI):
Top directory for writing files : SSTrandom_assembly
For writing result files :
SSTrandom_assembly/SSTrandom_d_results
For writing result info files : SSTrandom_assembly/SSTrandom_d_info
For writing tmp files : SSTrandom_assembly/SSTrandom_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : SSTrandom_assembly/SSTrandom_d_chkpt

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

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

Result files:
Saved as CAF (orc) : yes
Saved as MAF (orm) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : no
Saved as GFF3 (org3) : no
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : yes
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 : SSTrandom_out.caf
MAF : SSTrandom_out.maf
FASTA : SSTrandom_out.unpadded.fasta
FASTA quality : SSTrandom_out.unpadded.fasta.qual
FASTA (padded) : SSTrandom_out.padded.fasta
FASTA qual.(pad): SSTrandom_out.padded.fasta.qual
GAP4 (directory): SSTrandom_out.gap4da
ACE : SSTrandom_out.ace
HTML : SSTrandom_out.html
Simple text : SSTrandom_out.txt
TCS overview : SSTrandom_out.tcs
Wiggle : SSTrandom_out.wig
------------------------------------------------------------------------------
Creating directory SSTrandom_assembly ... done.
Creating directory SSTrandom_assembly/SSTrandom_d_results ... done.
Creating directory SSTrandom_assembly/SSTrandom_d_info ... done.
Creating directory SSTrandom_assembly/SSTrandom_d_chkpt ... done.
Creating directory SSTrandom_assembly/SSTrandom_d_tmp ... done.

Tmp directory is not on a NFS mount, good.

Localtime: Mon Jun 15 16:35:43 2015

Loading reads from /home/user/Desktop/SST/random.fastq type fastq
Localtime: Mon Jun 15 16:35:43 2015
Loading data from FASTQ file: /home/user/Desktop/SST/random.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)


Done.
Loaded 1800000 reads, Localtime: Mon Jun 15 16:35:47 2015
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Checking reads for trace data (loading qualities if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
No SCF data present in any read, EdIt automatic contig editing for Sanger data
is now switched off.
1800000 reads with valid data for assembly.
Localtime: Mon Jun 15 16:35:49 2015

Generated 1800000 unique DNA template ids for 1800000 valid reads.
No useful template information found.
TODO: Like Readpool: strain x has y reads
Have read pool with 1800000 reads.

===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 1800000 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 1729095 0 0 0 0 0
Avg tot rlen 0 0 162 0 0 0 0 0
Avg rlen used 0 0 168 0 0 0 0 0
W/o clips 0 0 1800000 0 0 0 0 0

IonTor total bases: 293136450 used bases in used reads: 291375003
===========================================================================


Checking pairs of readgroup 1 (named: 'SSTiontorrent'): found 0
SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_clippings_t0.0.txt
SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_clippings_t1.0.txt
SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_clippings_t2.0.txt
SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_clippings_t3.0.txt
Post-load clips:
Localtime: Mon Jun 15 16:35:50 2015
Writing temporary hstat files:
freemem: 28912746496
TNH: 5356
XME 1: 0.000212828
XME 2: 0.1
NEPB 1: 104857
NEPB 2: 104857
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Mon Jun 15 16:35:50 2015

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon Jun 15 16:35:50 2015
clean up temporary stat files...Localtime: Mon Jun 15 16:35:50 2015
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Mon Jun 15 16:35:50 2015
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
CLIP MSG: Adaptor right found: 910
CLIP MSG: Partial adaptor right found: 2

===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 1800000 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 1729068 0 0 0 0 0
Avg tot rlen 0 0 162 0 0 0 0 0
Avg rlen used 0 0 168 0 0 0 0 0
W/o clips 0 0 1799088 0 0 0 0 0

IonTor total bases: 293136450 used bases in used reads: 291347891
===========================================================================


Sorting reads ... done.

Tmp directory is not on a NFS mount, good.

PRED MAXTID 1799999
Hash analysis for proposed cutbacks:Localtime: Mon Jun 15 16:35:58 2015
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Mon Jun 15 16:36:57 2015

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon Jun 15 16:37:38 2015
clean up temporary stat files...Localtime: Mon Jun 15 16:37:38 2015
Raw MHI: 15655676
Raw avg. freq. : 69
HSS 18140202 HSST: 16326182
Localtime: Mon Jun 15 16:37:41 2015
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 69
Corrected avg. raw frequency coverage: 69

Final average frequency: 69

Deduced thresholds:
-------------------
Min normal cov: 27.6
Max normal cov: 110.4
Repeat cov: 131.1
Heavy cov: 552
Crazy cov: 1380
Mask cov: 6900

Repeat ratio histogram:
-----------------------
0 13903120
1 3046790
2 1091878
3 78846
4 6334
5 3236
6 3900
7 3574
8 1982
9 456
10 80
22 6
=========================================================

Assigning statistics values:
Localtime: Mon Jun 15 16:37:42 2015
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Mon Jun 15 16:37:51 2015
Localtime: Mon Jun 15 16:37:51 2015

Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 187026
Num reads cliped right: 541681
Num reads completely killed: 99015
Total bases clipped : 11440984

Clipping dubious poly-base stretches at end of reads ... Hash analysis for
proposed cutbacks:Localtime: Mon Jun 15 16:37:52 2015
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Mon Jun 15 16:38:49 2015

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon Jun 15 16:39:28 2015
clean up temporary stat files...Localtime: Mon Jun 15 16:39:28 2015
Raw MHI: 15655087
Raw avg. freq. : 69
HSS 18139558 HSST: 16325603
Localtime: Mon Jun 15 16:39:31 2015
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 69
Corrected avg. raw frequency coverage: 69

Final average frequency: 69

Deduced thresholds:
-------------------
Min normal cov: 27.6
Max normal cov: 110.4
Repeat cov: 131.1
Heavy cov: 552
Crazy cov: 1380
Mask cov: 6900

Repeat ratio histogram:
-----------------------
0 13902524
1 3046742
2 1091878
3 78846
4 6334
5 3236
6 3900
7 3574
8 1982
9 456
10 80
22 6
=========================================================

Assigning statistics values:
Localtime: Mon Jun 15 16:39:31 2015
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Mon Jun 15 16:39:41 2015
Localtime: Mon Jun 15 16:39:41 2015

Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 12
Num reads cliped right: 64
Num reads completely killed: 8
Total bases clipped : 1207

Clipping dubious poly-base stretches at end of reads ...
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 1800000 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 1700962 0 0 0 0 0
Avg tot rlen 0 0 162 0 0 0 0 0
Avg rlen used 0 0 165 0 0 0 0 0
W/o clips 0 0 1113519 0 0 0 0 0

IonTor total bases: 293136450 used bases in used reads: 280996451
===========================================================================


Performing snapshot 1
Localtime: Mon Jun 15 16:39:43 2015
Creating directory SSTrandom_assembly/SSTrandom_d_chkpt ... done.
Localtime: Mon Jun 15 16:39:55 2015
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 5870
Ngid: 0
Pid: 5870
PPid: 5869
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 64
Groups: 4 24 27 30 46 108 124 1000
VmPeak: 4898680 kB
VmSize: 4636520 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 4597596 kB
VmRSS: 4596780 kB
VmData: 4623500 kB
VmStk: 136 kB
VmExe: 5792 kB
VmLib: 0 kB
VmPTE: 9024 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/256785
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 456
nonvoluntary_ctxt_switches: 30109
--------------------------------------------------------------------------------


Pass: 1 / 5

===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 1800000 0 0 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 1700962 0 0 0 0 0
Avg tot rlen 0 0 162 0 0 0 0 0
Avg rlen used 0 0 165 0 0 0 0 0
W/o clips 0 0 1113519 0 0 0 0 0

IonTor total bases: 293136450 used bases in used reads: 280996451
===========================================================================


Localtime: Mon Jun 15 16:39:55 2015
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done
Localtime: Mon Jun 15 16:40:55 2015

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon Jun 15 16:41:35 2015
clean up temporary stat files...Localtime: Mon Jun 15 16:41:36 2015
Raw MHI: 13573022
Raw avg. freq. : 80
HSS 15959752 HSST: 14363777
Localtime: Mon Jun 15 16:41:38 2015
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 80
Corrected avg. raw frequency coverage: 80

Final average frequency: 80

Deduced thresholds:
-------------------
Min normal cov: 32
Max normal cov: 128
Repeat cov: 152
Heavy cov: 640
Crazy cov: 1600
Mask cov: 8000

Repeat ratio histogram:
-----------------------
0 11762414
1 3138364
2 989570
3 51228
4 5206
5 3512
6 4074
7 3960
8 1116
9 252
10 4
11 8
12 6
14 10
15 4
19 2
22 2
23 2
24 4
25 2
27 8
28 4
=========================================================

Estimator of average coverage: 80
Assigning statistics values:
Localtime: Mon Jun 15 16:41:38 2015
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Mon Jun 15 16:41:56 2015
Buntifying reads (this may take a while) ... done.
Adding fork tags (this may take a while) ... done.
Writing read repeat info to:
SSTrandom_assembly/SSTrandom_d_info/SSTrandom_info_readrepeats.lst ... 248
sequences with 256 masked stretches.
AS_resumeasembly 0
AS_resumeisok 0
fileExists(SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_signal_findpossibleoverlaps_pass.1.ok)
0
Localtime: Mon Jun 15 16:41:59 2015


Searching for possible overlaps:
Localtime: Mon Jun 15 16:41:59 2015
Now running threaded and partitioned skimmer with 19 partitions in 4 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.

truncating SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_posmatchf_pass.1.bin
truncated SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_posmatchf_pass.1.bin
from 1854957864 to 919751160

truncating SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_posmatchc_pass.1.bin
truncated SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_posmatchc_pass.1.bin
from 1782413736 to 857481240


Hits chosen: 148102700

Localtime: Mon Jun 15 16:51:52 2015

Total megahubs: 0
Cutting back possible chimeras ... done.
Chimeras were searched for ... looking for hits to purge.
truncating
SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_posmatchf_pass.1.bin from
919751160 to 919737504
truncating
SSTrandom_assembly/SSTrandom_d_tmp/SSTrandom_int_posmatchc_pass.1.bin from
857481240 to 857467920
System memory: 33679417344
Mem2keepfree: 5051912601
Used by MIRA: 5499346944
Mem avail: 23128157799
rsh increased memtouse to: 23128157799
Edge vector capacity: 155510474
Can load up to 155505474 skim edges at once.
Partitioning into 1 blocks.
Blocks: 1800000
We have 148100452 skims in file.
Localtime: Mon Jun 15 16:51:54 2015
De-normalising SKIM hits ... (this will take a while)
Localtime: Mon Jun 15 16:52:01 2015
Localtime: Mon Jun 15 16:52:23 2015
Writing normalised skimblock 0 ( 4.4 GiB) ... done.
Localtime: Mon Jun 15 16:52:47 2015
Loading block 0
Only one block, already loaded.
Localtime: Mon Jun 15 16:52:47 2015
Step 0
Loading block 0
Only one block, already loaded.
Localtime: Mon Jun 15 16:53:09 2015
Only long reads
Step 10
Loading block 0
Only one block, already loaded.
Total skims taken: 7030690
Step 20
Loading block 0
Only one block, already loaded.
Total skims taken: 7030690
Step 30
Loading block 0
Only one block, already loaded.
Total skims taken: 12102308
Step 40
Loading block 0
Only one block, already loaded.
Total skims taken: 12102308
Step 50
Total skims taken: 12102308
Step 53
Loading block 0
Only one block, already loaded.
Total skims taken: 21990829
Step 55
Loading block 0
Only one block, already loaded.
Total skims taken: 21991821
Step 60
Loading block 0
Only one block, already loaded.
Total skims taken: 21991858
Step solexa by critlevel
rsh4_takeSolexaByCritLevel.
Loading block 0
Only one block, already loaded.
Taken 0 hits.
rsh4_takeSolexaByCritLevel.
Loading block 0
Only one block, already loaded.
Taken 0 hits.
Step template overlaps
Loading block 0
Only one block, already loaded.
Step NAO
rsh4_takeNeedAllOverlaps.
None needed.
Total skims taken: 21991858

Filtering forward skims.
Localtime: Mon Jun 15 16:54:19 2015
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Filtering complement skims.
Localtime: Mon Jun 15 16:54:30 2015
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done all filtering.
Localtime: Mon Jun 15 16:54:41 2015
Making alignments.
Localtime: Mon Jun 15 16:54:41 2015

Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 12058287
Calculated: 6576589
Evaded (PB): 1
Rejected (checkfun): 0
Trans 100 saved: 5481697

Banned overlap pairs: 31568 in 20714 sets.

Localtime: Mon Jun 15 17:01:53 2015

Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Alignment stats:
Potential: 9933571
Calculated: 5669530
Evaded (PB): 112
Rejected (checkfun): 0
Trans 100 saved: 4263929

Banned overlap pairs: 61073 in 36907 sets.

Localtime: Mon Jun 15 17:08:06 2015

Localtime: Mon Jun 15 17:08:06 2015
Counting number of alignments in file ... done.
Expecting 21930672 alignments.
Localtime: Mon Jun 15 17:08:07 2015
Loading confirmed 21930672 overlaps from disk (will need approximately 1.2 GiB
RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Found 72 banned facts.
Localtime: Mon Jun 15 17:08:31 2015
Resizing pool to 21930600 overlaps.


Sorting confirmed overlaps (this may take a while) ... done.

Localtime: Mon Jun 15 17:08:36 2015
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: Mon Jun 15 17:08:38 2015

Writing clusters:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Writing unclustered reads ... done.
Localtime: Mon Jun 15 17:08:39 2015
BFC: 1 0
TGS: 1800000
overlapcompressstepping: 100000
nextoverlapcompress: 100000
Moving small clusters to debris:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done. 272 reads moved to debris.
bfc 1
Localtime: Mon Jun 15 17:08:41 2015

bfc 2
Timing BFC prelim1: 18
bfc 3
bfc 4
Timing BFC discard con: 2
bfc 5
bfc 6/0
bfc 7/0
Building new contig 1
Localtime: Mon Jun 15 17:08:41 2015
Unused reads: 1700288
bfc 8/0
0 Known 1: 0
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
Timing priv_initialiseLowerBoundOEdges: 189848
Timing priv_fdns_subFillCache 1 1 1 1 : 1454536
Startcache size: 4891
hit unlooked threshold
Timing priv_fdns_genome total: 1454772
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 666
pft 12 / 363
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 940
pft 10 / 117
[121] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++a+++ 1002
pft 11 / 122
[179] ++++++++++++++++a++aa+++++++++++++++a+++++++++++++++++++++++ 1088
pft 14 / 124
[235] ++++a++++++a++a+++++a++++++++++++++++++++++a++++a+++++++++++ 1152
pft 14 / 120
[289] +++++++++++aa++++a+a+++++++++++++++++a++++++++a+++++++++++++ 1198
pft 18 / 115
[343] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1242
pft 14 / 113
[403] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 1567
pft 12 / 116
[462] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1819
pft 10 / 118
[522] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 1867
pft 16 / 127
[581] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 2151
pft 12 / 123
[640] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2422
pft 10 / 124
[700] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2551
pft 10 / 130
[760] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2690
pft 13 / 132
[820] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 2737
pft 18 / 124
[879] +++++++++++++++++++++++++++++++++a++++++++a+++++++++++++++++ 2752
pft 18 / 100
[937] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 2760
pft 19 / 88
[996] +++++++++++++++++++++++++++++d++++++++++++++++++++++++++++++ 2945
pft 18 / 97
[1055] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3178
pft 10 / 119
[1115] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3290
pft 12 / 122
[1175] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 3513
pft 11 / 120
[1234] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3780
pft 11 / 123
[1294] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4021
pft 13 / 141
[1354] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4149
pft 12 / 126
[1414] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 4165
pft 18 / 125
[1473] ++++aa++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4186
pft 18 / 123
[1531] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4197
pft 22 / 98
[1591] +++++++++++++++++++++++++++++++++++++++++++++++++++++a++++++ 4208
pft 18 / 102
[1650] ++++++++++++++++++++++++++++++++++++a+++++++++a+++++++++++++ 4214
pft 20 / 99
[1708] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4215
pft 17 / 81
[1768] ++a+++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 4380
pft 15 / 97
[1826] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4549
pft 11 / 130
[1886] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4842
pft 11 / 128
[1946] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5060
pft 12 / 129
[2006] ++++++++++++++++++++++++++++++++++++++++++a++a++++++++++++++ 5073
pft 18 / 110
[2064] ++++++++++++++++++++++++++++++++d+++++++++++++++++++++++++++ 5113
pft 23 / 92
[2123] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5340
pft 11 / 119
[2183] ++++++++++++++++++++++++++++++++++++++++++ad++++++++++++++++ 5350
pft 17 / 83
[2241] ++++d+++++++++a+++++++++++++d+++++++++++++++++++++++++++++++ 5564
pft 13 / 119
[2298] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5764
pft 11 / 118
[2358] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5999
pft 11 / 123
[2418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6062
pft 12 / 130
[2478] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 6082
pft 17 / 130
[2537] +a++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 6108
pft 22 / 98
[2595] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6173
pft 21 / 75
[2655] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 6313
pft 15 / 118
[2714] ++++++++++++++++++++++++++aa++++++++++++++++++++++++++++++++ 6635
pft 10 / 119
[2772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7050
pft 13 / 101
[2832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7307
pft 11 / 120
[2892] +++++++++++++++++++++++++++++++++++++a++++++++++++++++a+++++ 7359
pft 17 / 103
[2950] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7562
pft 12 / 109
[3010] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 7642
pft 13 / 136
[3069] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 7772
pft 13 / 103
[3128] +++++++++++++++++++++++++++++++++++++++++a+++a++++++++++++++ 7869
pft 12 / 113
[3186] +++++++++a++++++++++++++++++++++++aaa+++++++++++++++++++++++ 7894
pft 13 / 129
[3242] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7971
pft 14 / 147
[3302] ++++++++++++++++a++++++++++++++++++++++++++++++++++++++++aa+ 7980
pft 20 / 147
[3359] +++++++++++++++++++++++a++++a++++++a++++++++++++++++++++++++ 7991
pft 29 / 126
[3416] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 7997
pft 22 / 98
[3475] ++++++++GGG++++GG+G+++G++GG+G++GG+GGG+++G+++GGG++G+++G++++++ 8003
pft 9 / 106
[3514] +++++G++++++++G++++++++++G++++++++++++++++++++++++++++++++++ 8009
pft 19 / 106
[3571] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8324
pft 17 / 143
[3631] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8677
pft 11 / 117
[3691] ++++++++++++++++++++++++++++++++++d+++++++++++++++++++++++++ 8739
pft 15 / 110
[3750] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8745
pft 19 / 129
[3810] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 8751
pft 22 / 131
[3869] +++++++aaaaaaaaaaaaaaaaaaaaaaaa+daaaaaaaaa++++a+aaaa++++aaa+ 8758
pft 74 / 120
[3887] +a+a+++++++++++++++aaaapriv_ld addRead: 495695
priv_ld total: 554316
Timing BFC paf construct: 2199050

ccon timings:
cct pre 2878
cct dir 5488
cct xcu 14307
cct tmp 2135
cct sw 311624
cct pic 2061
cct ico 126220
cct icm 0
cct upd 2406
cct del 0
cct rmz 2311
cct gcp 488

ccon i timings (3902):
ccit insglcc 236
ccit insglaro 950
ccit insglact 107
ccit insgltot 4024
ccit pr 25512
ccit templ 3140
ccit index 2111
ccit biglccins 3606
ccit biglinterpol 861
ccit biglupdtags 509
ccit biglfpcri 449
ccit bigllgap 17352
ccit biglshiftread 4091
ccit bigltot 49667
ccit insgr 2221
ccit ucv 20522

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3903
Triggering additional cluster check: shouldmovesmallclusterstodebris
startCacheRanDry
Moving small clusters to debris:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done. 31 reads moved to debris.
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:45 2015
Timing BFC analysereadcov: 18958
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 19
mict_shadow 103
mict_fallout 8199
mict_newin 4644
mict_helper1 30487
mict_newin 4644
mict_restofloop 4766
mict_totalloop 66913
done.

-------------- Contig statistics ----------------
Contig id: 1
Contig length: 8758

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3903 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 194 0 0
0 0 0
Avg. coverage 0.000 0.000 83.072 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 194
Avg. contig coverage: 83.072

Consensus contains: A: 1344 C: 2604 G: 2594 T: 1308 N: 0
IUPAC: 0 Funny: 0 *: 908
GC content: 66.217%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 67615
Localtime: Mon Jun 15 17:08:45 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 72337 cases.

P 1, marked 72337 reads.
Timing BFC edit tricky1: 45655
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 48427
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1369 cases.

Edited 1369 reads.
Localtime: Mon Jun 15 17:08:45 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:45 2015
Timing BFC edit tricky2: 34248

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 353 positions.
Localtime: Mon Jun 15 17:08:45 2015
Deleting superfluous gap columns (2) ... done, deleted 581 columns.
Localtime: Mon Jun 15 17:08:45 2015
Timing BFC edit single discrepancy, no HAF: 77307
bfc 12/0
Timing BFC delPSHP: 881
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 20139
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 301
mict_pre 5
mict_shadow 116
mict_fallout 7742
mict_newin 4307
mict_helper1 28082
mict_newin 4307
mict_restofloop 4498
mict_totalloop 62116
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 157680
Contig coverage analysis ... Timing BFC loop total: 4239102
bfc 1
Localtime: Mon Jun 15 17:08:45 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 2
Localtime: Mon Jun 15 17:08:45 2015
Unused reads: 1696354
bfc 8/0
0 Known 1: 3903
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 594
pft 9 / 117
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 933
pft 9 / 122
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1166
pft 13 / 137
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1381
pft 11 / 125
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1609
pft 11 / 121
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1739
pft 13 / 133
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1790
pft 17 / 137
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1855
pft 17 / 127
[481] +++++++++++++++++++++++++a++++++++++++++++++++++++++++++++++ 1903
pft 18 / 113
[540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2016
pft 18 / 113
[600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2192
pft 23 / 79
[660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2563
pft 10 / 112
[720] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2876
pft 9 / 111
[780] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3105
pft 10 / 117
[840] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3386
pft 12 / 132
[900] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3573
pft 13 / 125
[960] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3879
pft 10 / 120
[1020] ++++++++++++++++++++++++++++a+++++++++++++++++++++++++a+++++ 3899
pft 15 / 113
[1078] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 3987
pft 16 / 112
[1136] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4310
pft 13 / 106
[1196] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4338
pft 17 / 110
[1256] ++a++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 4351
pft 18 / 97
[1314] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4362
pft 20 / 90
[1374] +a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 4376
pft 19 / 84
[1432] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 4382
pft 21 / 87
[1491] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4388
pft 20 / 83
[1551] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4886
pft 11 / 105
[1611] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5174
pft 10 / 119
[1671] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5350
pft 13 / 139
[1731] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5380
pft 13 / 136
[1791] +++++++++++++++a+++++++++++++a++++++++++++++++++++++++++++++ 5616
pft 13 / 125
[1849] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 5689
pft 15 / 138
[1908] ++++++++a++++++++++++++++++++++++++++++a+++++++++aa++++++a++ 5746
pft 17 / 120
[1963] ++++++a+++++++++a++++++++++++++++++++++++++++++++a++++++++++ 5765
pft 19 / 106
[2020] ++++++++++++++++a+++++++++++a++++++++a++++++++++++++++++++++ 5793
pft 15 / 97
[2077] ++++++++a+++++++++++++++++++++++++++++++++++++a+++++++++++++ 5816
pft 17 / 81
[2135] +++++++++++++++++++++++++a+++a++++++++++++++++++++++++++++++ 6054
pft 13 / 90
[2193] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6330
pft 10 / 117
[2253] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 6349
pft 13 / 122
[2312] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 6359
pft 16 / 110
[2371] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6551
pft 16 / 95
[2431] +++++++++++++++++a++++++++++++++++++++++++++++++++++++a+++++ 6586
pft 23 / 113
[2489] +++++++a++a++++++++++a++a+aaaadaaaa+aa++++++++++++++++++++++ 6787
pft 10 / 115
[2534] +++++a+++++++++++++++++++++++++++++++++++++++++++++++++aaa++ 7121
pft 11 / 102
[2590] +++++++++++++++++++++++++++++++++++++++++++++++++++++a++++++ 7188
pft 20 / 91
[2649] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7579
pft 16 / 116
[2709] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7582
pft 17 / 75
[2769] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 7936
pft 11 / 110
[2828] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8109
pft 14 / 89
[2888] ++++++++++a+++a++++++a+a++++++++++++++++a+++a+++++++++++++++ 8235
pft 10 / 111
[2942] +a++++++++a+++a+++++++++++++++++++++++++++++a+++++a++a++++++ 8244
pft 13 / 84
[2996] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 8395
pft 17 / 63
[3055] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8697
pft 10 / 117
[3115] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8739
pft 14 / 125
[3175] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 8836
pft 15 / 108
[3234] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9226
pft 16 / 112
[3294] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9577
pft 9 / 122
[3354] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9668
pft 14 / 122
[3414] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9732
pft 14 / 121
[3474] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10017
pft 11 / 119
[3534] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 10026
pft 10 / 129
[3593] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10034
pft 13 / 113
[3652] ++++++++++++aaaaaa+aa+a+++aa+++a++++a+aaa+aaaa+aaa+aa++aaaad 10045
pft 6 / 129
[3681] d++++++d+++++++d+++ddadad+++d+aaaad+adadaadaaaa++aa+adaaaaaa 10049
pft 6 / 110
[3706] +aaa+d++++aaa+++++++++++++++++++++++++++++++++++++++++++++++ 10381
pft 9 / 106
[3759] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10564
pft 11 / 122
[3819] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10576
pft 18 / 117
[3879] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11023
pft 12 / 109
[3939] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11312
pft 13 / 136
[3999] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11458
pft 11 / 124
[4059] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11492
pft 15 / 128
[4119] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11561
pft 17 / 128
[4179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11578
pft 20 / 113
[4239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11602
pft 24 / 84
[4299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11850
pft 15 / 103
[4359] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 11969
pft 12 / 121
[4418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12330
pft 10 / 115
[4478] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12420
pft 11 / 126
[4538] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12436
pft 16 / 124
[4598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12452
pft 20 / 114
[4658] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 12454
pft 19 / 81
[4717] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12459
pft 26 / 87
[4777] ++++++++++++++++++++++++++++++aa+++++++++a++++++++a+++++++++ 12467
pft 22 / 100
[4833] ++++++++d+a+a+++++++++++++++++++++++++++++++++++++++++++++++ 12946
pft 17 / 126
[4890] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13082
pft 14 / 122
[4950] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13334
pft 11 / 121
[5010] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13620
pft 11 / 120
[5070] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13817
pft 10 / 131
[5130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14078
pft 9 / 128
[5190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14124
pft 12 / 132
[5250] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14171
pft 14 / 131
[5310] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 14204
pft 18 / 112
[5369] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 14256
pft 19 / 106
[5428] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 14280
pft 17 / 84
[5487] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 14333
pft 21 / 102
[5546] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14839
pft 10 / 120
[5606] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14999
pft 10 / 126
[5666] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15190
pft 11 / 121
[5726] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 15241
pft 17 / 115
[5785] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15376
pft 18 / 92
[5845] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15462
pft 11 / 125
[5905] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 15539
pft 12 / 132
[5964] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15673
pft 13 / 124
[6024] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15712
pft 18 / 112
[6084] ++++a++++++++++++++++++++++++++++++++++++++++++++a+++++++a++ 15728
pft 10 / 142
[6141] ++++++++++++++++++++++++++aaa+++++++++aa++++++++++++++++++++ 15739
pft 9 / 132
[6196] ++++++++++++++++++++++++++a+a++++++aa++++++++aa+++++++++++++ 15746
pft 14 / 162
[6250] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15753
pft 24 / 158
[6310] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 15767
pft 27 / 162
[6369] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15776
pft 24 / 143
[6428] +++++++++++++++a+++++++++++++++a++++++++++++++++++++++++++++ 15803
pft 25 / 127
[6486] +++++++++++++++++++++++++++++++aa++++++++++++++a++++++++++++ 15810
pft 21 / 111
[6543] +++++++++ad++++++++++++++++++++++++++++++G+++++++++++++++G++ 15816
pft 25 / 124
[6599] +a++++++++++++++++++++++++++++++++aa++++aaa++++++++++++aaaa+ 15819
pft 25 / 110
[6649] +++++++G++G+++++G++G++++++++++++++G++++a+++++++++++G+++++++G 15828
pft 19 / 131
[6701] +++++G++++++++GG+++G++GGG+a++++a++++++++++++++++++++++d+++++ 15833
pft 16 / 137
[6751] +a+++++++++++++++++++++++++++++++++++++++++a++++++++++++aaaa 15837
pft 25 / 143
[6805] +aa++a+a+++++aaaaaa+++++aaa++++a++++aa+a+++a+a++a+d++++++++G 15844
pft 28 / 134
[6842] G++G+G+GGGG+G+G+++++++++++++++++++++++++++++++++++++++++++++ 16692
pft 14 / 117
[6894] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16810
pft 13 / 120
[6954] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16817
pft 16 / 107
[7014] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16833
pft 13 / 107
[7074] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17124
pft 9 / 128
[7134] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17548
pft 10 / 123
[7194] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17686
pft 14 / 132
[7254] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17722
pft 14 / 123
[7314] ++++++++++++++++++++++++++++++++++++++a+a+a+++++a+++++++++++ 17819
pft 14 / 122
[7370] +++++++++++++a++a+++a+++++++++++++a+++++a+++aa++a+++aa++++++ 17833
pft 13 / 105
[7420] +++++a++++++++a+++++a++a++++a++++a+a+aa+++++++++++++a+++++++ 17878
pft 12 / 104
[7470] +a+aaa++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18255
pft 14 / 127
[7526] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18433
pft 12 / 119
[7586] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18467
pft 13 / 118
[7646] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 18524
pft 14 / 117
[7705] ++a++a+++++a++++++++++++d++++++++++a+++++++a+a++++++++++++++ 18581
pft 15 / 98
[7758] +++a++++++++++a++++++aa+++++++++++++++++++++++++++++++++++++ 18743
pft 11 / 119
[7814] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18815
pft 12 / 137
[7874] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 18871
pft 11 / 119
[7933] ++++++++++a+++++a+a+++++++++++++++++++++++a+++a+++++++a+++++ 18894
pft 11 / 117
[7986] a++++++ad++a++++a+++a+++++++++++++++++++++++++++++++++++++++ 19185
pft 10 / 114
[8041] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19258
pft 15 / 120
[8101] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19448
pft 12 / 123
[8161] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19574
pft 17 / 171
[8221] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 19620
pft 14 / 121
[8280] +d++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19959
pft 13 / 123
[8339] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20122
pft 11 / 125
[8399] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 20369
pft 12 / 123
[8458] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20528
pft 11 / 131
[8518] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20577
pft 14 / 139
[8578] ++++++++++++++++++a++++++++++++++a++++++++++++++++++++++++++ 20638
pft 13 / 127
[8636] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21109
pft 10 / 116
[8696] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21263
pft 12 / 124
[8756] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21338
pft 11 / 129
[8816] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21361
pft 12 / 126
[8876] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21402
pft 17 / 131
[8936] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21471
pft 14 / 111
[8996] +++++++++a+++aaaaaa+++++++aa++aa++++++++++aa+++a+a++++++++++ 21477
pft 13 / 120
[9041] ++++++++++++++++++a+++++++++++++++++++++++++++++++aa++++++a+ 21537
pft 17 / 138
[9097] +a++++++++++++++++++++++++++++++++++++++++++++++++++a++++++a 21547
pft 11 / 136
[9154] ++a+++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 21564
pft 10 / 148
[9212] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21808
pft 11 / 121
[9272] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 21832
pft 12 / 118
[9331] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 21945
pft 11 / 109
[9390] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 22330
pft 11 / 109
[9450] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 22527
pft 11 / 118
[9510] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 22784
pft 11 / 108
[9569] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 22867
pft 13 / 139
[9629] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 22913
pft 14 / 122
[9688] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 22955
pft 11 / 134
[9747] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 22972
pft 12 / 148
[9807] +++++++++++++++++++++++a++++++++++++++++a++++a++++++++++++++ 22984
pft 11 / 139
[9864] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23061
pft 12 / 147
[9924] ++++++++++a++++++++++++++d+++++++++a+++a++++++aaa+++++++++++ 23072
pft 10 / 137
[9977] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 23075
pft 13 / 150
[10036] +++++++++++++++++++++a++++++++++++++++++++++++a+++++++++++++ 23080
pft 17 / 153
[10094] +++++++++++++++++++++++++++++++++++a++++++++++++a+++++++++++ 23088
pft 17 / 155
[10152] +++++++++++++++++a+++++++++++++++++++++a++++++++++++++++++++ 23251
pft 17 / 144
[10210] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23491
pft 12 / 130
[10270] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23568
pft 10 / 128
[10330] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 23774
pft 11 / 144
[10389] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 23808
pft 9 / 134
[10448] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23810
pft 10 / 146
[10508] ++++++++++++++++++++++++++++++a+++++a+++++++++++++++++++++++ 23820
pft 20 / 164
[10566] +++++++++a++++++++++++++++++++++++++++++++++++++++++aa++++++ 23823
pft 19 / 151
[10623] +++++++++a+++++++++++++++++++++++++a++++++++++++++++++++a+++ 23830
pft 20 / 152
[10680] ++++++++++++++++++++a++++++++++++++++a+++++++++++++++++++++a 23846
pft 16 / 164
[10737] +++++++++++++++++++++++++a+++++++++a++++++++++++++++++++++++ 23852
pft 25 / 151
[10795] +++++++a+++++++++++++++++++++++++++++++++++++++++a++++++++++ 23860
pft 20 / 173
[10853] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23866
pft 22 / 151
[10913] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 23879
pft 23 / 160
[10972] ++a+++++++++++++++++++++++++++++++++++++++a++a+++++++++a++++ 23885
pft 22 / 137
[11028] +++a+++++++++++++a++++++++++++a++++++++++++++++++++++++a++++ 23892
pft 20 / 136
[11084] ++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++ 23904
pft 22 / 139
[11143] ++++++++++++++++++++a++++++++++++a++++++++++++++++++++++++++ 23907
pft 21 / 120
[11201] +++++++++++++++++++++a+++++a++++++++++++++++++++++++++++++aa 23910
pft 21 / 116
[11257] ++++++a+++++++++++++++++++++a+++++++++++++++++++++++++++++++ 23918
pft 22 / 132
[11315] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23927
pft 23 / 123
[11375] ++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 23930
pft 20 / 113
[11434] ++++++++++++++a+++a+++++++++++++++++++++++++++++++++++++++++ 23934
pft 45 / 127
[11492] +++++++++++++++++++++++++++++++++++++da++aaa+aaaaaa+aaaaaaaa 23940
pft 26 / 116
[11532] aaaa+aaaadaaaaaadadaaaaaaaddaddaadaaaaadaa++++++++++++++++++ 23941
pft 9 / 103
[11552] ++++++++++++++++++++++a+aaaa+aa+aaaaaaaa+aaaada+aaaaaaaa+aaa 23942
pft 12 / 126
[11579] aaaaaaaaaaaa+aa+aaaa++daaaaa+aaaaaaa+a++++++++a+++++++++++++ 23947
pft 15 / 116
[11607] +++++++++++++++++++++++++++++++++++++++++++++++++++++aa+++++ 23965
pft 36 / 138
[11665] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 23968
pft 20 / 159
[11725] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 23983
pft 45 / 170
[11784] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++G+ 23989
pft 35 / 116
[11842] ++G+++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 24258
pft 15 / 144
[11900] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 24265
pft 14 / 133
[11960] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 24273
pft 17 / 150
[12020] ++++++++++++++a+++++++d+d+aaa+ada++++a++adda++ada+ad++a+d+a+ 24276
pft 9 / 137
[12057] d+aaa+a+++++++++++++++++d+d++++++++a+daa++a+aaaaa+aa+++a++++ 24278
pft 7 / 136
[12098] +++++a+++a++++da+a+++aa++a+a+++++aaa+aa+aa++a+aaa+aa+aadaa++ 24278
pft 9 / 130
[12131] +++++aaa+++adaadaaa+aaaa+a+aa+aadadaaaadaaaa+aaaaaaaaa+aaaaa 24280
pft 6 / 136
[12144] aaaaaaaaaaaaaaaaa+aa+aaa+aa+aaa+a+aa+daaaaa+aa+aaaaaaaaaaaaa 24283
pft 4 / 124
[12153] aaaaaaaaad+aa+a+aaa+a+a++a++a+aa+aa+a++aaaa++a++aaaaaaa+++aa 24289
pft 6 / 131
[12174] adaaaaa+daa+daaaaaaaaaaaaaaa++++aa+a+a+++++++aaaaa+aadaaaa+a 24290
pft 5 / 113
[12192] ++a+++aaa++a++++++a+a++++aa++a++aaaa+a++++aa++aaa+aaa+a+++a+ 24298
pft 9 / 144
[12227] ++a++++++++++++++a++da++a++aaaaaaa+++++++++++++a++++++++a+++ 24302
pft 11 / 143
[12273] +++++aaa++++a+++++++a+aa+++++a+++++++++d+++++aa+++++++a+++++ 24309
pft 18 / 177
[12321] ++++++++++++++++a++aa+++++a+++++a++++++++++++++++++a++++a+a+ 24314
pft 21 / 149
[12373] +++++++++++++++++++++++++++++++++++++++d+++++++++++a+a++aa++ 24324
pft 16 / 147
[12427] a++++++++++++++++++++a++++++++++aa+a++d+++a+++++++++++++++++ 24338
pft 30 / 152
[12481] +++aaada+++a+++++++a+a++++++d++a+aa++++++++a+++++++++++++a++ 24347
pft 27 / 126
[12527] ++++++a+++a+++a++a++++++++++ad+aaa++++++++a+aaaaaa+++a++++a+ 24348
pft 22 / 94
[12569] ++++++++++++++++++++++++++a+++a+++a+a+++a+++a++++++++++a+a++ 24349
pft 24 / 75
[12620] GGG+aG+G+++++GG+Ga+GG+GGGGaGGaGGGG+GGGGGaGGGGG+GaGGGaGG+G++G 24354
pft 10 / 119
[12635] GGG+GGaGG+GGGGGG++++++++GGaGGG++G++G+G+GGGGG+GG+GG++++Ga++GG 24357
pft 16 / 100
[12659] GGGG+G+GaG+GG++++G+GGGGGG++G+GGaGG+G+G++GGG++GGG++GG+G+++G++ 24362
pft 17 / 91
[12685] +G+++GGGGGGGG++GGGa+GG+a+G+++G++GGGGa+G+G+G+GG+GGGG+Ga++++++ 24363
pft 29 / 74
[12710] aaaaaaG+++GGaa++GGG+aG+G++++GGGGGGG++++aa++a++GGGGGGG++++GGG 24366
pft 38 / 80
[12733] GG+G++a+GaGa++G+++G+a+GGG+aG++GGGGGGGGG++++++GG++++GGGG+a+++ 24367
pft 37 / 63
[12762] +a+G+Ga++aaa+++GGGGGGGGGGGGG+++aa+++GGGGGGGGGGGG+++++++G++++ 24492
pft 19 / 94
[12786] GG+GGGG+GG+G+GGGGG++GGGG+GGGGGGGGG++++G++Ga++GGG+GGGGG+G+GGG 24503
pft 5 / 90
[12804] GGGG+GG+++++++++++++++++++++++++++++++++++++++++++++++++++++ 24966
pft 11 / 112
[12859] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 25035
pft 13 / 134
[12919] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 25200
pft 12 / 136
[12979] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 25271
pft 11 / 136
[13039] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 25341
pft 14 / 124
[13099] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 25355
pft 13 / 126
[13159] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 25429
pft 13 / 117
[13218] ++++++++++d+++++++++++++++++++++++++++++++++++++++++++++++++ 25650
pft 11 / 124
[13277] ++++++a+++++++++++++a++++++++++++++++++++++++++++++a++++++++ 25752
pft 10 / 134
[13334] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 25764
pft 9 / 131
[13394] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 26134
pft 14 / 135
[13454] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 26313
pft 10 / 121
[13514] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 26611
pft 10 / 119
[13574] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 26709
pft 16 / 131
[13634] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 26747
pft 18 / 123
[13694] ++++++++++++a++++++++++++++++++++++++++++++++++++++a++++++++ 26807
pft 15 / 111
[13752] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 26882
pft 17 / 99
[13812] ++++++++++++++++++++d+a+++++++++++++++++++++++++++++++++++++ 27196
pft 12 / 123
[13870] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27231
pft 11 / 130
[13930] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27236
pft 18 / 141
[13990] +++++++++++++++++++++++++++++++d++++++++++++++++++++++a+++a+ 27334
pft 12 / 127
[14046] a++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 27346
pft 13 / 136
[14105] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 27351
pft 18 / 133
[14164] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27359
pft 13 / 136
[14224] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27368
pft 21 / 135
[14284] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27374
pft 14 / 148
[14344] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27382
pft 23 / 156
[14404] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27391
pft 30 / 135
[14464] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 27430
pft 22 / 151
[14524] ++++++++++++++++a++++++a+++++++++++++a+++++++++++++++++++a++ 27445
pft 36 / 145
[14580] ++++++++++++++++++++++++++++++G++++++++++G++G++++GG+++G++G++ 27449
pft 22 / 109
[14633] ++G++GGG++G++++G+++GGa+G++++G+G+++GG+++GG++G++++GGG++G+G++++ 27460
pft 18 / 120
[14670] G+G++a+++++++++++++GG++++++G++GG++G+++++++G++++++++++G+G+++G 27469
pft 31 / 114
[14718] +++++GG+G++++G++++++++G+GG+++++G++G+++++++++++++++++++++++++ 27480
pft 44 / 97
[14769] +++++GGGGGGa++++G++++G+++++++++++GG++G++GGG+GG+GG+aa+GGaa+aa 27483
pft 32 / 72
[14801] aGa+Gaaa+a+d+++++a+a+ad+++d+++dda++dd+ad++d+a+a++ada+aa+daad 27486
pft 545 / 128
[14828] a+++a++a+a+++++dd+dd+a+adaaaa+daa+aaaaddaaadaaa++aaaaaaaaaaa 27494
pft 15 / 123
[14847] +a++aaa+a++aa+daaa+daaa+a+a++a+a+++aa+a+aaaaa++++++a+aa+aaa+ 27497
pft 25 / 121
[14874] +++aa+aaaaa++a+++adaaad+a+aaaaaa+aaa++aa++da+++aaa++++a+++++ 27500
pft 16 / 144
[14901] aaaaa++++aaaaaaa+aaaaaa+++a+aa+++aaad+a+++a+aa+aaa+d+ad+aaaa 27500
pft 14 / 124
[14922] aaa+aaadaaaaaa++++aaa++aaa++ad+aa++a+aa++a+a++a+++aaaaaaaaaa 27501
pft 22 / 140
[14943] aaaaaaaa+aaa+a+aa+aaaaaaaaaaaaaaa+ad+aaaaaa+aaa+aa++adaaaa++ 27504
pft 19 / 147
[14956] ++++aaaaaaaaaaa+a+++aaaaaaadaaaa++daaa++aada+aG+aa+aaaaGaaa+ 27505
pft 13 / 129
[14972] +aaa++++d++a++++++daad+++++a+aaaaaa+aaaaaaaaaadaaaaaaaaaaaaa 27508
pft 42 / 146
[14991] aa+aaaaaaaa+aaaaa+aa++aa++++++++++++++a+++a+++++++d++a+++a++ 27508
pft 32 / 146
[15027] aa++++aa+aa+aa++aaaaaaa++aa+aaaa+++da+++a+a+aaaaa+a++daaa+G+ 27513
pft 57 / 145
[15052] ++++++++++++++++++++++++++++++++++++++++GGGG++G+++aG+GGaG+a+ 27515
pft 19 / 158
[15100] +aG++GG+aG+G+aaaGGGaaaGGaaG+a+G+GGGa+GGGGGGGGGGGG+a+++G+GGGG 27517
pft 53 / 124
[15114] GGGGGGGG++GaG++GG+GGGGGGaGGGaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 27517
pft 29 / 111
[15119] aGGaGaaaaaaaaaaaaaaaGGGGaaGGGGGGGGGGGGGGGGG+aaGaGaaaGaGa+a++ 27517
pft 249 / 91
[15124] +a+dd++aaa+d++++ad+aa+adaaadaaaa+aa+aaaa+aaaaaaa+aaaadaa+aa+ 27518
pft 10 / 126
[15140] aaaaaaaaaaa+a+aaaaaaaaaaaaa+aaaaaaaaadadaaaaaaaaa+aaaaaaaaaa 27518
pft 4 / 111
[15144] aaaaddddaaaa+a+daaaaaaaaaaaaaaaadaaaadaaaaaadaaaaaaaaaaaaaaa 27518
pft 4 / 112
[15146] aaaaaa+aaaaaaaaa+aaaaaaaaaaaaaaaaaa+aaaaaaaa+aaaaad+aaaaaaaa 27518
pft 4 / 128
[15151] aaaaaaaaadaaaaaaadaaaaaaaaaaaaaaaa+aaaaaaa+aaaaaaaaadadaaaaa 27518
pft 4 / 121
[15153] aaaaaaaadaaa+d+aaaGGGGGGGGGGGGGGaGGGaaaaaaaaGaaGGGaa+aaaGGGG 27519
pft 4 / 104
[15156] GaaaaaaGGGGGaaaaaa+daa+adaaaaa+aaaaaaad+aaaaadaadaa+aaaaaaaa 27520
pft 84 / 100
[15161] adaaaadaa+aaadaadaaaada+aaaaaddaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 27521
pft 4 / 122
[15163] aaaaaa+aaaaaaaaaaaaaaaaaaaaaadaaaaaaaaaaaaaaaaaGGGGaaGaaGGGG 27521
pft 4 / 120
[15164] GGaaaaaaaaadGaapriv_ld addRead: 2194456
priv_ld total: 2508056
Timing BFC paf construct: 2508117

ccon timings:
cct pre 12847
cct dir 19549
cct xcu 84257
cct tmp 9238
cct sw 1384996
cct pic 8460
cct ico 538346
cct icm 0
cct upd 9632
cct del 0
cct rmz 9182
cct gcp 9798

ccon i timings (15163):
ccit insglcc 815
ccit insglaro 2980
ccit insglact 356
ccit insgltot 14296
ccit pr 100093
ccit templ 15978
ccit index 8170
ccit biglccins 18428
ccit biglinterpol 3096
ccit biglupdtags 1877
ccit biglfpcri 1671
ccit bigllgap 88949
ccit biglshiftread 16847
ccit bigltot 235606
ccit insgr 8554
ccit ucv 81770

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 15164
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:47 2015
Timing BFC analysereadcov: 71170
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 12
mict_shadow 725
mict_fallout 29958
mict_newin 15141
mict_helper1 120894
mict_newin 15141
mict_restofloop 15158
mict_totalloop 240001
done.

-------------- Contig statistics ----------------
Contig id: 2
Contig length: 27521

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 15164 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 278 0 0
0 0 0
Avg. coverage 0.000 0.000 105.026 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 278
Avg. contig coverage: 105.026

Consensus contains: A: 4341 C: 7856 G: 7750 T: 4191 N: 0
IUPAC: 0 Funny: 0 *: 3383
GC content: 64.653%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 243279
Localtime: Mon Jun 15 17:08:48 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 314257 cases.

P 1, marked 314257 reads.
Timing BFC edit tricky1: 205830
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 221 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 244806
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 1467 positions.
Localtime: Mon Jun 15 17:08:48 2015
Deleting superfluous gap columns (2) ... done, deleted 464 columns.
Localtime: Mon Jun 15 17:08:48 2015
Timing BFC edit single discrepancy, no HAF: 217274
bfc 12/0
Timing BFC delPSHP: 4269
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: 9399
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 986
mict_pre 6
mict_shadow 755
mict_fallout 29434
mict_newin 14770
mict_helper1 119522
mict_newin 14770
mict_restofloop 14936
mict_totalloop 237561
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 715587
Contig coverage analysis ... Timing BFC loop total: 4230334
bfc 1
Localtime: Mon Jun 15 17:08:49 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 3
Localtime: Mon Jun 15 17:08:49 2015
Unused reads: 1681190
bfc 8/0
0 Known 1: 15164
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 510
pft 14 / 129
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 709
pft 11 / 131
[121] +++++++++++++++++++++a+++++++++++++++++++++++a++++++++++++++ 808
pft 15 / 112
[179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1138
pft 10 / 119
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1473
pft 11 / 119
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1538
pft 13 / 120
[359] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 1632
pft 14 / 127
[418] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 1711
pft 15 / 121
[477] +++++++++++a+++++++++++++++++++++++++a++++++++++++++++++a+++ 1746
pft 15 / 111
[534] +++++a++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 1768
pft 15 / 100
[592] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 1997
pft 14 / 114
[651] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2240
pft 10 / 123
[711] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2444
pft 11 / 122
[771] +++++a++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 2601
pft 15 / 136
[829] +++++++++++++++++++++aaa++++++a++++++++a++++++++++++++++++++ 2793
pft 12 / 118
[884] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3054
pft 11 / 116
[944] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3081
pft 13 / 128
[1004] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3102
pft 19 / 133
[1064] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3273
pft 13 / 117
[1124] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3296
pft 18 / 119
[1184] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3333
pft 19 / 113
[1244] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3345
pft 21 / 100
[1304] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3368
pft 20 / 77
[1364] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 3408
pft 20 / 101
[1422] a++++++++++++++++++++++++++++a++++++++++++++++++++++++++a+++ 3444
pft 15 / 120
[1480] +++a++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3915
pft 14 / 131
[1539] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 3947
pft 14 / 127
[1598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4014
pft 13 / 127
[1658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4048
pft 15 / 111
[1718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4078
pft 15 / 135
[1778] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 4279
pft 10 / 147
[1837] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 4284
pft 23 / 143
[1896] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4422
pft 10 / 127
[1956] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4523
pft 10 / 140
[2016] +++++++++++++++++++++a+++++++++++++++++++++++++++++a++++++++ 4530
pft 21 / 126
[2074] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4539
pft 17 / 123
[2134] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4546
pft 15 / 121
[2194] +++++++++++++++++++++++++++++++++++++++++++++++a+++++++++G++ 4550
pft 15 / 148
[2252] ++++++++++++++++++++G+++++++GG+G+++GG+++++++++++++++++++++++ 4555
pft 13 / 148
[2306] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4576
pft 21 / 155
[2366] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4589
pft 38 / 138
[2426] +a++++++++++G+++GG+G+++++++++++GG+++++++++G++++++G+++++++++G 4594
pft 16 / 142
[2476] ++++G+++++++++++++++++++a++++++++++++++++++++++++++++++++GGG 4603
pft 30 / 123
[2530] GGG+GG+G+GG++G+G+GGGGGGGGGGGGGG++GGGG+G+GGG++GGG+++GG+GGGGG+ 4603
pft 6 / 106
[2549] +G++++G+GG++GGGGGGGG+G+G+++++GG+GG++G+GGGGG+G+++GG+GG+GGG+G+ 4605
pft 13 / 89
[2576] +G+G++GGG++GG+GG+G++GGGGG++GGGG++GG+++G++Ga+GG+GG+G+++++GGGG 4605
pft 15 / 71
[2602] GGGG+G+++++++G++G+G+G+GGGGGGGGGGGGGGG++GGGG+++++GG+++G+GGGGG 4608
pft 26 / 60
[2626] GGGGGGGGGGGGG++G++++G+G+GGGGGGGGGGGGGGGGaaaaaaaaaaaaaaaaaaaa 4608
pft 84 / 73
[2634] GGGGGGG+aGGaGGGGGGG+GGG++GGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGG 4608
pft 7 / 103
[2638] GGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 4608
pft 76 / 80
[2638] GGGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 365365
priv_ld total: 414557
Timing BFC paf construct: 414695

ccon timings:
cct pre 2190
cct dir 3378
cct xcu 13655
cct tmp 1658
cct sw 230983
cct pic 1415
cct ico 89061
cct icm 0
cct upd 1682
cct del 0
cct rmz 1628
cct gcp 999

ccon i timings (2637):
ccit insglcc 99
ccit insglaro 370
ccit insglact 42
ccit insgltot 2214
ccit pr 16945
ccit templ 2248
ccit index 1388
ccit biglccins 2429
ccit biglinterpol 557
ccit biglupdtags 325
ccit biglfpcri 315
ccit bigllgap 12895
ccit biglshiftread 2659
ccit bigltot 37635
ccit insgr 1506
ccit ucv 14212

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2638
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:50 2015
Timing BFC analysereadcov: 12080
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 8
mict_shadow 81
mict_fallout 4998
mict_newin 2442
mict_helper1 20683
mict_newin 2442
mict_restofloop 2511
mict_totalloop 40466
done.

-------------- Contig statistics ----------------
Contig id: 3
Contig length: 4608

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2638 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 188 0 0
0 0 0
Avg. coverage 0.000 0.000 108.489 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 188
Avg. contig coverage: 108.489

Consensus contains: A: 742 C: 1277 G: 1262 T: 738 N: 0
IUPAC: 0 Funny: 0 *: 589
GC content: 63.175%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 40900
Localtime: Mon Jun 15 17:08:50 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 54876 cases.

P 1, marked 54876 reads.
Timing BFC edit tricky1: 31932
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 36592
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1016 cases.

Edited 1016 reads.
Localtime: Mon Jun 15 17:08:50 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:50 2015
Timing BFC edit tricky2: 23589

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 219 positions.
Localtime: Mon Jun 15 17:08:50 2015
Deleting superfluous gap columns (2) ... done, deleted 330 columns.
Localtime: Mon Jun 15 17:08:50 2015
Timing BFC edit single discrepancy, no HAF: 49981
bfc 12/0
Timing BFC delPSHP: 716
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 16280
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 184
mict_pre 6
mict_shadow 83
mict_fallout 4677
mict_newin 2297
mict_helper1 19072
mict_newin 2297
mict_restofloop 2345
mict_totalloop 37549
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 107795
Timing BFC loop total: 736511
bfc 1
Localtime: Mon Jun 15 17:08:50 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 4
Localtime: Mon Jun 15 17:08:50 2015
Unused reads: 1678552
bfc 8/0
0 Known 1: 2638
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 643
pft 11 / 114
[61] +++++++++++++++++++++++++++++++++++aa++++++++++aa+++++++++++ 685
pft 12 / 124
[117] ++++a+++a++++++++++++++++++++a++++a+++++++a+++++++++a+aa++++ 731
pft 11 / 125
[169] ++++++++++a+++++a+++a++++++++++++a++++++++a+++++++++++++++++ 812
pft 12 / 111
[224] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 970
pft 14 / 96
[283] ++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 1225
pft 10 / 113
[342] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1483
pft 10 / 113
[402] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1506
pft 17 / 123
[462] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1762
pft 15 / 111
[522] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1994
pft 13 / 131
[582] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2123
pft 10 / 124
[642] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2179
pft 16 / 136
[702] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2190
pft 20 / 113
[762] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2205
pft 21 / 98
[822] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2244
pft 20 / 81
[882] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++d+ 2532
pft 12 / 115
[940] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2710
pft 11 / 116
[1000] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2845
pft 11 / 130
[1060] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3041
pft 13 / 121
[1120] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3237
pft 11 / 129
[1180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3282
pft 16 / 104
[1240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3318
pft 18 / 92
[1300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3708
pft 10 / 138
[1360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3866
pft 9 / 122
[1420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4013
pft 13 / 128
[1480] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 4082
pft 15 / 118
[1539] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4485
pft 10 / 114
[1598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4655
pft 10 / 128
[1658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4691
pft 15 / 119
[1718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4702
pft 20 / 98
[1778] ++++++++++++++++++a++++++++++++++++++a+++++a++++++++++++++++ 4719
pft 20 / 68
[1835] +++++++++++a++++++++++++++++a+++++++++++++++++++++++++++++++ 4973
pft 15 / 119
[1893] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5317
pft 10 / 114
[1953] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5448
pft 12 / 128
[2013] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 5524
pft 12 / 125
[2072] +++++++++++++++++++++a+++++++++++++++++a++++++++++++++++++++ 5587
pft 21 / 122
[2130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5783
pft 16 / 106
[2190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5895
pft 12 / 133
[2250] +a++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6157
pft 11 / 114
[2308] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6245
pft 13 / 122
[2368] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6295
pft 13 / 118
[2428] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6410
pft 18 / 101
[2488] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6598
pft 14 / 107
[2548] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 6611
pft 9 / 132
[2607] ++ad++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6968
pft 14 / 120
[2665] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6983
pft 22 / 92
[2725] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 6993
pft 10 / 145
[2784] ++++++++++++++++++++++++++++++++++aaaa++++++++++++++++++++++ 7002
pft 13 / 166
[2840] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7005
pft 22 / 151
[2900] +++++a++++++++++++++++++++++++++++++++++++++++++a++++++++a++ 7013
pft 30 / 134
[2957] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7020
pft 20 / 116
[3017] ++++++++++++++++++++++++++a+++++++++a+++++++++++++++++++++++ 7026
pft 25 / 151
[3075] ++++++++++++++++a++++++++++++a+++++++++++++++++++++a++++++++ 7030
pft 29 / 116
[3132] ++aaaaaaaaaaaaaa+aaaaaaaaaaaaaaaadaaaaaaaaaapriv_ld addRead: 390020
priv_ld total: 434355
Timing BFC paf construct: 434429

ccon timings:
cct pre 2327
cct dir 3832
cct xcu 12047
cct tmp 1684
cct sw 240145
cct pic 1718
cct ico 103571
cct icm 0
cct upd 1944
cct del 0
cct rmz 1919
cct gcp 310

ccon i timings (3133):
ccit insglcc 193
ccit insglaro 732
ccit insglact 85
ccit insgltot 3151
ccit pr 19977
ccit templ 2735
ccit index 1682
ccit biglccins 3170
ccit biglinterpol 698
ccit biglupdtags 398
ccit biglfpcri 388
ccit bigllgap 15246
ccit biglshiftread 3481
ccit bigltot 42216
ccit insgr 1751
ccit ucv 16694

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3134
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:50 2015
Timing BFC analysereadcov: 14458
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 96
mict_fallout 6822
mict_newin 3805
mict_helper1 26271
mict_newin 3805
mict_restofloop 3846
mict_totalloop 56002
done.

-------------- Contig statistics ----------------
Contig id: 4
Contig length: 7030

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3134 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 188 0 0
0 0 0
Avg. coverage 0.000 0.000 84.261 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 188
Avg. contig coverage: 84.261

Consensus contains: A: 1129 C: 2086 G: 2023 T: 1051 N: 0
IUPAC: 0 Funny: 0 *: 741
GC content: 65.336%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 56711
Localtime: Mon Jun 15 17:08:50 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 59015 cases.

P 1, marked 59015 reads.
Timing BFC edit tricky1: 37209
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 38211
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1207 cases.

Edited 1207 reads.
Localtime: Mon Jun 15 17:08:51 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:51 2015
Timing BFC edit tricky2: 28110

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 301 positions.
Localtime: Mon Jun 15 17:08:51 2015
Deleting superfluous gap columns (2) ... done, deleted 477 columns.
Localtime: Mon Jun 15 17:08:51 2015
Timing BFC edit single discrepancy, no HAF: 62057
bfc 12/0
Timing BFC delPSHP: 529
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 17816
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 306
mict_pre 6
mict_shadow 90
mict_fallout 6265
mict_newin 3482
mict_helper1 23574
mict_newin 3482
mict_restofloop 3615
mict_totalloop 50799
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 127819
Contig coverage analysis ... Timing BFC loop total: 820060
bfc 1
Localtime: Mon Jun 15 17:08:51 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 5
Localtime: Mon Jun 15 17:08:51 2015
Unused reads: 1675418
bfc 8/0
0 Known 1: 3134
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 513
pft 10 / 123
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 756
pft 11 / 123
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 824
pft 12 / 132
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1000
pft 15 / 131
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1142
pft 13 / 126
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1188
pft 18 / 119
[361] +++++++++++++++++++++++++++++++++++++++++++++++a++++++++++++ 1250
pft 17 / 125
[420] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 1374
pft 21 / 122
[479] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1503
pft 10 / 123
[539] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1669
pft 12 / 127
[599] +a+++++++++++++++++++++++++++++++a++++++++++++a+++++++++++++ 1705
pft 21 / 102
[656] +++++++++a+++++++++++++++++++a++++++++++++++++++++++a+++++++ 1710
pft 19 / 90
[713] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 1867
pft 18 / 77
[772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2068
pft 10 / 118
[832] ++++++++++++a++++++a++++a+++++++++++++++++++++++++++++++++++ 2323
pft 11 / 119
[889] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2413
pft 15 / 118
[949] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2643
pft 10 / 123
[1009] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 2668
pft 14 / 138
[1068] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2808
pft 11 / 122
[1128] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 2821
pft 20 / 127
[1186] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2831
pft 23 / 115
[1246] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2835
pft 20 / 97
[1306] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 2842
pft 21 / 81
[1365] +++++++++++++++++++++++++++++++++++++a+d++++++++++++++++++++ 3050
pft 18 / 99
[1423] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3187
pft 11 / 108
[1483] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3567
pft 11 / 111
[1543] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3738
pft 10 / 139
[1603] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3749
pft 17 / 104
[1663] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 4122
pft 15 / 94
[1722] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4347
pft 10 / 117
[1782] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4445
pft 12 / 126
[1842] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4509
pft 15 / 135
[1902] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4645
pft 14 / 127
[1962] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4650
pft 19 / 101
[2022] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 4927
pft 14 / 89
[2081] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5177
pft 11 / 111
[2141] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5526
pft 14 / 94
[2201] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5859
pft 12 / 114
[2261] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 6133
pft 10 / 113
[2320] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6386
pft 10 / 120
[2380] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6516
pft 13 / 127
[2440] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6580
pft 16 / 122
[2500] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6835
pft 14 / 113
[2560] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6910
pft 14 / 125
[2620] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6942
pft 21 / 107
[2680] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6955
pft 19 / 92
[2740] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6975
pft 22 / 99
[2800] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7035
pft 16 / 126
[2860] +++++++aa+++++++++++++++++++++++++++a+++++++++++++++++++++++ 7042
pft 24 / 129
[2917] ++++++++++++++GG+GG+GGGGG+GGGGGGGGGG+G+GG+G+GGGGG+GGGG+GGGGG 7045
pft 10 / 79
[2939] G+GGGGG+GGGG+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG+GGG++++++++++++ 7047
pft 6 / 85
[2956] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7065
pft 27 / 140
[3016] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 7441
pft 16 / 113
[3075] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7569
pft 12 / 129
[3135] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7641
pft 16 / 129
[3195] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 7652
pft 16 / 111
[3254] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8036
pft 11 / 99
[3313] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8451
pft 10 / 111
[3373] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8587
pft 13 / 122
[3433] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8622
pft 20 / 122
[3493] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8858
pft 14 / 82
[3553] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9047
pft 10 / 117
[3613] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9166
pft 12 / 128
[3673] ++++++++++++++++a++++++++++++++++++++++++++++++++a++++++++++ 9191
pft 16 / 120
[3731] ++++++++++++++++++++a++++a++++++++++++++++++++++++++++++++++ 9293
pft 15 / 103
[3789] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9434
pft 15 / 122
[3849] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9761
pft 13 / 137
[3909] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9898
pft 11 / 128
[3969] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9983
pft 16 / 135
[4029] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10001
pft 14 / 117
[4089] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10090
pft 13 / 124
[4149] ++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 10142
pft 12 / 162
[4208] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10557
pft 9 / 137
[4268] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10808
pft 11 / 119
[4328] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10920
pft 12 / 131
[4388] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10958
pft 14 / 125
[4448] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 10970
pft 17 / 113
[4507] +++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 10985
pft 15 / 106
[4566] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11371
pft 11 / 96
[4626] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11466
pft 16 / 122
[4686] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11568
pft 13 / 115
[4746] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11670
pft 13 / 123
[4806] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 11678
pft 11 / 148
[4865] ++++++++++++a++++++++++++++++++++++++++++++++++++++a++++++++ 11684
pft 22 / 145
[4923] +++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++ 11691
pft 13 / 146
[4982] ++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11697
pft 16 / 157
[5041] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11709
pft 35 / 156
[5101] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11711
pft 12 / 158
[5161] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11717
pft 20 / 158
[5221] +++++++++++++++++++++++++++++++++++++++++++++++++++++a++++++ 11725
pft 31 / 134
[5280] +++++++++++++++++++++++++++++a+++GG++GGG++++G+++++++++GG+GGG 11730
pft 17 / 109
[5328] +G++G+++G+++G++++++++++++GG+GG++GGGGG+G+++G+++++GG++G+GGGGGG 11738
pft 19 / 123
[5364] +G+GGG+++GG++G+++++++G+G+G+G++G++++++++GG+GG++++G+G++GGGGGGG 11744
pft 36 / 88
[5398] GGGGGGGGGGGGGG+++G++++GGGG+++++++++++++++++aaaaaaaaaa+aaaaa+ 11745
pft 142 / 95
[5425] +++++++++++++++++++a+G+G++a+++++++aa++++++++++++++++++++++++ 11746
pft 34 / 165
[5479] +++++++++++++++++++a+++G+GG+GGGGG+GGGGGGGGGGGGGGGGGGGGGGGG++ 11746
pft 64 / 119
[5505] aGGGGGGGaGGGGGGGGGGGGGGGGGpriv_ld addRead: 702022
priv_ld total: 789567
Timing BFC paf construct: 789628

ccon timings:
cct pre 4157
cct dir 9071
cct xcu 21806
cct tmp 3046
cct sw 431781
cct pic 3048
cct ico 184594
cct icm 0
cct upd 3409
cct del 0
cct rmz 3263
cct gcp 899

ccon i timings (5504):
ccit insglcc 153
ccit insglaro 591
ccit insglact 83
ccit insgltot 4177
ccit pr 35098
ccit templ 5064
ccit index 2955
ccit biglccins 5533
ccit biglinterpol 1215
ccit biglupdtags 715
ccit biglfpcri 684
ccit bigllgap 28147
ccit biglshiftread 5306
ccit bigltot 77771
ccit insgr 3257
ccit ucv 29424

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 5505
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:52 2015
Timing BFC analysereadcov: 25576
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 10
mict_shadow 161
mict_fallout 11689
mict_newin 6326
mict_helper1 45267
mict_newin 6326
mict_restofloop 6582
mict_totalloop 95197
done.

-------------- Contig statistics ----------------
Contig id: 5
Contig length: 11746

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 5505 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 216 0 0
0 0 0
Avg. coverage 0.000 0.000 88.663 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 216
Avg. contig coverage: 88.663

Consensus contains: A: 1803 C: 3514 G: 3397 T: 1721 N: 0
IUPAC: 0 Funny: 0 *: 1311
GC content: 66.229%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 96547
Localtime: Mon Jun 15 17:08:52 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 107700 cases.

P 1, marked 107700 reads.
Timing BFC edit tricky1: 69116
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 73564
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1966 cases.

Edited 1966 reads.
Localtime: Mon Jun 15 17:08:52 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:52 2015
Timing BFC edit tricky2: 50534

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 531 positions.
Localtime: Mon Jun 15 17:08:52 2015
Deleting superfluous gap columns (2) ... done, deleted 810 columns.
Localtime: Mon Jun 15 17:08:52 2015
Timing BFC edit single discrepancy, no HAF: 115326
bfc 12/0
Timing BFC delPSHP: 1223
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 30533
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 560
mict_pre 6
mict_shadow 173
mict_fallout 10815
mict_newin 5958
mict_helper1 42538
mict_newin 5958
mict_restofloop 5972
mict_totalloop 89026
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 229626
Contig coverage analysis ... Timing BFC loop total: 1486802
bfc 1
Localtime: Mon Jun 15 17:08:52 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 6
Localtime: Mon Jun 15 17:08:52 2015
Unused reads: 1669913
bfc 8/0
0 Known 1: 5505
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 498
pft 11 / 112
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 596
pft 13 / 129
[121] +++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++a 625
pft 13 / 118
[179] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 898
pft 12 / 121
[238] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1015
pft 12 / 128
[298] ++++++++++a+++++++++++++++++++++++a++++++++++a++++++++++++++ 1036
pft 11 / 133
[355] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 1100
pft 13 / 120
[414] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1525
pft 10 / 114
[474] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1667
pft 9 / 120
[534] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1969
pft 12 / 132
[594] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2105
pft 12 / 126
[654] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2305
pft 11 / 123
[714] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2337
pft 14 / 128
[774] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 2417
pft 18 / 132
[833] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2459
pft 18 / 121
[893] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++a+++ 2491
pft 16 / 118
[951] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2518
pft 17 / 100
[1011] +++++++++++++++++++++++aa+++++++++++++++++++++++++a+++++++++ 2569
pft 15 / 98
[1068] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2894
pft 12 / 121
[1128] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3003
pft 12 / 132
[1188] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3156
pft 11 / 139
[1247] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 3413
pft 13 / 132
[1306] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 3424
pft 15 / 119
[1365] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 3485
pft 15 / 106
[1424] ++++++++++++++++++++++++++++++++++++++++a+++++++++++a+++++++ 3552
pft 16 / 138
[1482] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3940
pft 11 / 127
[1542] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4006
pft 14 / 139
[1602] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4056
pft 16 / 108
[1662] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4470
pft 12 / 114
[1722] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4733
pft 9 / 130
[1782] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5043
pft 10 / 124
[1842] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5189
pft 13 / 117
[1902] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 5319
pft 11 / 118
[1961] ++++++++++++++++++++++++++++++++++++++++aa+++a+++aa++a+++a+a 5484
pft 13 / 147
[2012] aa+++aa+a+aaaaa++++a+a++aaaa+a+a++++a++++++++a+++a++++++++++ 5496
pft 14 / 114
[2052] +a++a++a++++++a+++++++++++++++++++++++++++++++a+a+++++++++++ 5508
pft 17 / 104
[2105] a+++++++a++++++a+++++++++++++++++a+a++a+aaa++a++aaaa+a+a+++a 5622
pft 11 / 106
[2149] +a+++++++aa++a++a+++++++a++++a+++++++++aa++++++++a++++++a+a+ 5690
pft 9 / 112
[2197] +++a+++++++a+++aa+++++a++++a++a++++++++a+a++++++++++a+++++a+ 5713
pft 13 / 97
[2246] +++a++++++++++++++++++++++++++++a+++++++++++a+++++++++++++++ 5730
pft 16 / 85
[2303] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 5889
pft 14 / 100
[2362] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6160
pft 10 / 122
[2422] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6377
pft 10 / 124
[2482] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6694
pft 10 / 120
[2542] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6928
pft 11 / 121
[2602] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7170
pft 10 / 121
[2662] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7486
pft 10 / 135
[2722] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7676
pft 12 / 136
[2782] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7835
pft 11 / 129
[2842] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7883
pft 14 / 146
[2902] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8066
pft 12 / 135
[2962] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 8094
pft 17 / 138
[3021] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8145
pft 19 / 129
[3081] ++++++++++++++++a++++++++++++++++++++++a++++++++++++++++++++ 8162
pft 20 / 114
[3139] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 8216
pft 19 / 113
[3198] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8256
pft 19 / 102
[3258] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8544
pft 13 / 109
[3318] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 8593
pft 12 / 128
[3377] ++++++++++a++++++++++++++++++++++++++++++++++a++++++++++++++ 8664
pft 18 / 156
[3435] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8716
pft 15 / 119
[3495] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8749
pft 19 / 99
[3555] ++++++++a+++++a+++++++++++++++++++++++++++++++++++++++++++++ 8767
pft 18 / 93
[3613] +++++a++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 8797
pft 21 / 99
[3671] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 8914
pft 17 / 145
[3730] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 8933
pft 10 / 147
[3789] +++++++++++++++++++++++++++++++++a++++++++++++++++++++a+++++ 8939
pft 11 / 137
[3847] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8943
pft 13 / 149
[3907] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8950
pft 21 / 157
[3967] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 8964
pft 29 / 162
[4026] ++++++++++++++++++++++++++++++++++a++++++++++++a+++++++a++++ 8974
pft 28 / 164
[4083] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 9297
pft 13 / 127
[4142] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9404
pft 13 / 136
[4201] a+++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 9599
pft 10 / 130
[4260] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9606
pft 15 / 114
[4320] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9618
pft 14 / 110
[4380] ++++++++++++++++++++++++++++++a++++++++++a++++++++++++++++++ 9626
pft 30 / 141
[4438] ++++++++++++++++++++++++++++a++++++++++++++++++++++++a++++++ 9795
pft 19 / 113
[4496] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10175
pft 10 / 118
[4556] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10421
pft 10 / 112
[4616] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10677
pft 12 / 104
[4676] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10958
pft 9 / 115
[4736] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11000
pft 13 / 131
[4796] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 11022
pft 21 / 138
[4855] +++++a+++++++++++++++++++++++++++++++++++++++++++a++a+++++++ 11028
pft 21 / 78
[4912] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11338
pft 13 / 100
[4972] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11491
pft 12 / 127
[5032] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11720
pft 18 / 83
[5092] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11958
pft 10 / 121
[5152] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12061
pft 12 / 123
[5212] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12218
pft 12 / 124
[5272] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12372
pft 12 / 124
[5332] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12412
pft 12 / 132
[5392] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 12490
pft 16 / 104
[5451] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12813
pft 15 / 105
[5511] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 12898
pft 12 / 141
[5570] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12916
pft 11 / 141
[5630] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 13259
pft 15 / 125
[5689] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13458
pft 11 / 126
[5749] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13638
pft 11 / 124
[5809] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13828
pft 14 / 116
[5869] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14056
pft 12 / 123
[5929] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14147
pft 12 / 124
[5989] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14390
pft 10 / 125
[6049] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14705
pft 9 / 121
[6109] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14963
pft 12 / 116
[6169] ++++++++++++a+++++++++++++++++++++++++++++++++++++++a+++++++ 15011
pft 15 / 120
[6227] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15196
pft 13 / 123
[6287] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15269
pft 14 / 141
[6347] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15506
pft 16 / 118
[6407] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15723
pft 10 / 113
[6467] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16106
pft 9 / 115
[6527] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16341
pft 10 / 124
[6587] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16521
pft 10 / 124
[6647] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16755
pft 12 / 121
[6707] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++a+ 16810
pft 13 / 131
[6765] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16835
pft 19 / 130
[6825] +++++++++++++a+++++a+++++++++++++++++++++++++++a++++++++++++ 16888
pft 18 / 122
[6882] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 16925
pft 17 / 106
[6941] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 16939
pft 19 / 105
[7000] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16973
pft 23 / 125
[7060] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17003
pft 19 / 97
[7120] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17006
pft 16 / 98
[7180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17048
pft 18 / 129
[7240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17071
pft 18 / 154
[7300] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 17078
pft 9 / 149
[7359] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17082
pft 15 / 167
[7419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17087
pft 20 / 153
[7479] +a++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 17092
pft 21 / 137
[7537] +++++++++++++a+++++a+++++++++++++++++a++++++++++++++++++++a+ 17099
pft 26 / 123
[7593] +++++a+++++++++++++++++++++++++++++a+++++++++++++++++++++a++ 17104
pft 23 / 106
[7649] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17109
pft 28 / 123
[7709] +++aGG++++++++++a++++++++++++++++++++++++++++++++++G+GG++GG+ 17116
pft 20 / 107
[7760] +G++G+GGGG+G+G++++aa+++++G++++++G+++++a++++++++++++++++a+a++ 17118
pft 17 / 109
[7804] G++++++++++++GG+++++++++++++++++++++++++++a+++++++++++++++++ 17125
pft 20 / 121
[7861] ++++++++++++++++++++a++++++++++++++aa+a+aaa+++++++++++++++++ 17132
pft 16 / 153
[7914] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17142
pft 29 / 171
[7974] ++++++++++++++++++++a+++++++++++++++++a+++++++++++++++++++++ 17151
pft 45 / 119
[8032] ++++++++++++++++GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 17169
pft 10 / 71
[8047] G+++G+G+++++++++++++++++++++++++++++++++++++++++++++++a++a++ 17176
pft 21 / 147
[8103] ++++++++++++++++++++++++++++++aa++++++++++++GGG+G+++GG+aG+GG 17184
pft 26 / 105
[8150] GGGGGGGGG+G+GGGGG+GGGG+++G+a++a+aaaaddaaaaaaaaaaaaaaaaaa+G++ 17186
pft 11 / 93
[8164] ++GG+G+++++GG+aaaaaaaaa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 17186
pft 120 / 119
[8173] aaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 17186
pft 4 / 100
[8174] aaaaaaaaaaaaaaaaGaaGGGGGG+++aa+++aaGGGGGGGGGGGGGGGGGGGGGGGGG 17186
pft 13 / 109
[8180] GaGGaGGaGaaGGGGGGGGGGGaaaaaaaaaaa+GGG+GG+GGGGGGGGGGGGGGGGGGG 17189
pft 75 / 95
[8183] GGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 1087810
priv_ld total: 1213901
Timing BFC paf construct: 1213972

ccon timings:
cct pre 6429
cct dir 11655
cct xcu 37438
cct tmp 4660
cct sw 666961
cct pic 4514
cct ico 289080
cct icm 0
cct upd 5145
cct del 0
cct rmz 4892
cct gcp 1912

ccon i timings (8182):
ccit insglcc 479
ccit insglaro 1791
ccit insglact 208
ccit insgltot 8055
ccit pr 54092
ccit templ 8015
ccit index 4464
ccit biglccins 11707
ccit biglinterpol 1818
ccit biglupdtags 1087
ccit biglfpcri 1023
ccit bigllgap 47088
ccit biglshiftread 9280
ccit bigltot 125415
ccit insgr 4724
ccit ucv 44503

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 8183
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:53 2015
Timing BFC analysereadcov: 38344
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 9
mict_shadow 247
mict_fallout 17414
mict_newin 9503
mict_helper1 68587
mict_newin 9503
mict_restofloop 9415
mict_totalloop 142021
done.

-------------- Contig statistics ----------------
Contig id: 6
Contig length: 17189

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 8183 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 189 0 0
0 0 0
Avg. coverage 0.000 0.000 91.493 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 189
Avg. contig coverage: 91.493

Consensus contains: A: 2496 C: 5016 G: 5003 T: 2688 N: 0
IUPAC: 0 Funny: 0 *: 1986
GC content: 65.901%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 144079
Localtime: Mon Jun 15 17:08:54 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 165892 cases.

P 1, marked 165892 reads.
Timing BFC edit tricky1: 106759
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 109701
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 3060 cases.

Edited 3060 reads.
Localtime: Mon Jun 15 17:08:54 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:54 2015
Timing BFC edit tricky2: 78773

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 762 positions.
Localtime: Mon Jun 15 17:08:54 2015
Deleting superfluous gap columns (2) ... done, deleted 1239 columns.
Localtime: Mon Jun 15 17:08:54 2015
Timing BFC edit single discrepancy, no HAF: 178996
bfc 12/0
Timing BFC delPSHP: 2067
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 46750
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 795
mict_pre 6
mict_shadow 259
mict_fallout 16049
mict_newin 8693
mict_helper1 62993
mict_newin 8693
mict_restofloop 8702
mict_totalloop 130685
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 341581
Contig coverage analysis ... Timing BFC loop total: 2269691
bfc 1
Localtime: Mon Jun 15 17:08:55 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 2
bfc 5
bfc 6/0
bfc 7/0
Building new contig 7
Localtime: Mon Jun 15 17:08:55 2015
Unused reads: 1661730
bfc 8/0
0 Known 1: 8183
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 559
pft 9 / 119
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 829
pft 11 / 111
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 905
pft 17 / 142
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 954
pft 17 / 129
[241] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 1026
pft 17 / 118
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1216
pft 16 / 117
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1477
pft 13 / 112
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1677
pft 11 / 123
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1707
pft 12 / 118
[540] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 1721
pft 12 / 106
[599] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1776
pft 13 / 114
[659] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1797
pft 14 / 104
[719] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2022
pft 13 / 128
[779] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2032
pft 11 / 122
[839] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2046
pft 14 / 155
[899] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 2058
pft 29 / 129
[958] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 2064
pft 18 / 112
[1017] ++++++++G+++G+++G+G+++++++++++++++++++++++++++++++++++++++++ 2069
pft 17 / 134
[1073] ++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++ 2076
pft 28 / 138
[1132] ++++++++++GG+GGGGGGGGGGGG+GG+G+GG++GGGGGGG+GG++GGGG+G++++GGG 2083
pft 14 / 94
[1155] GGGGa+++GGG+GGGGGGGG+aaaaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 2083
pft 30 / 85
[1160] GGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 155771
priv_ld total: 174763
Timing BFC paf construct: 174847

ccon timings:
cct pre 923
cct dir 1299
cct xcu 6202
cct tmp 641
cct sw 97898
cct pic 643
cct ico 38200
cct icm 0
cct upd 744
cct del 0
cct rmz 723
cct gcp 317

ccon i timings (1159):
ccit insglcc 42
ccit insglaro 120
ccit insglact 15
ccit insgltot 900
ccit pr 7135
ccit templ 944
ccit index 617
ccit biglccins 860
ccit biglinterpol 232
ccit biglupdtags 152
ccit biglfpcri 135
ccit bigllgap 5887
ccit biglshiftread 1095
ccit bigltot 16001
ccit insgr 667
ccit ucv 6303

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1160
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:55 2015
Timing BFC analysereadcov: 5228
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 36
mict_fallout 2249
mict_newin 1124
mict_helper1 9195
mict_newin 1124
mict_restofloop 1121
mict_totalloop 18112
done.

-------------- Contig statistics ----------------
Contig id: 7
Contig length: 2083

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1160 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 185 0 0
0 0 0
Avg. coverage 0.000 0.000 106.382 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 185
Avg. contig coverage: 106.382

Consensus contains: A: 261 C: 594 G: 605 T: 376 N: 0
IUPAC: 0 Funny: 0 *: 247
GC content: 65.305%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 18345
Localtime: Mon Jun 15 17:08:55 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 23325 cases.

P 1, marked 23325 reads.
Timing BFC edit tricky1: 13771
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 16212
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 431 cases.

Edited 431 reads.
Localtime: Mon Jun 15 17:08:55 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:55 2015
Timing BFC edit tricky2: 10965

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 106 positions.
Localtime: Mon Jun 15 17:08:55 2015
Deleting superfluous gap columns (2) ... done, deleted 148 columns.
Localtime: Mon Jun 15 17:08:55 2015
Timing BFC edit single discrepancy, no HAF: 21365
bfc 12/0
Timing BFC delPSHP: 150
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 5998
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 89
mict_pre 5
mict_shadow 37
mict_fallout 2094
mict_newin 1038
mict_helper1 8434
mict_newin 1038
mict_restofloop 1032
mict_totalloop 16750
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 44456
Timing BFC loop total: 312323
bfc 1
Localtime: Mon Jun 15 17:08:55 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 8
Localtime: Mon Jun 15 17:08:55 2015
Unused reads: 1660570
bfc 8/0
0 Known 1: 1160
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 439
pft 15 / 127
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 597
pft 15 / 125
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 816
pft 10 / 126
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 899
pft 15 / 125
[241] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 927
pft 19 / 128
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 952
pft 19 / 111
[360] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 1360
pft 15 / 113
[419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1514
pft 11 / 125
[479] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1609
pft 15 / 124
[539] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1848
pft 10 / 124
[599] ++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 2150
pft 9 / 122
[658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2418
pft 9 / 122
[718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2697
pft 11 / 129
[778] +++++++++++++++++++++++++++++++++++++++a+++a++++++++++++++++ 2762
pft 16 / 146
[836] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2823
pft 20 / 135
[896] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 2880
pft 18 / 130
[955] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 2898
pft 20 / 112
[1014] +++++++a++++++++++++++++++++++++++++++++++a+++++++++++++++++ 2905
pft 17 / 109
[1072] ++++++++++++++++++++a+++++++++++++++++++++++++++++++a+++++++ 2921
pft 23 / 104
[1130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2933
pft 19 / 87
[1190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2937
pft 23 / 74
[1250] +a++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 3351
pft 13 / 91
[1308] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3780
pft 11 / 104
[1368] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3966
pft 11 / 116
[1428] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4056
pft 12 / 126
[1488] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4336
pft 12 / 138
[1548] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4379
pft 12 / 133
[1608] +++++++a++++++++++++++++++++++++++++++a+++++++++++++++++++++ 4399
pft 18 / 142
[1666] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4687
pft 12 / 123
[1726] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4732
pft 20 / 116
[1786] ++++++++++a+++++++++++++++++++++++++++a+++++++++++++++++++++ 4872
pft 17 / 105
[1844] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5219
pft 9 / 117
[1904] +++++++++++++++++++++++++a+++++++++++++++a++++++++++++++++++ 5299
pft 16 / 104
[1962] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 5305
pft 20 / 76
[2021] +++++++++a++++++a+++++++++++++++++++++++++++++++++++++++++++ 5733
pft 10 / 108
[2079] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6027
pft 11 / 116
[2139] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6168
pft 13 / 129
[2199] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6375
pft 14 / 123
[2259] +++++++++++++++++++++++++++++++a++++a++++++++a++++++++++++++ 6396
pft 19 / 144
[2316] +++++++++++++++++++++++++++++++++++++++++++++++++++++a++++++ 6457
pft 16 / 116
[2375] +++++++++++++++++++a+++++++++++a++++++++++++++++++++++++++++ 6544
pft 16 / 109
[2433] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6738
pft 12 / 118
[2493] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6819
pft 17 / 103
[2553] +++++++++++a+a+++++++++++++++++++++++++++++++++++++++++++a++ 6824
pft 18 / 80
[2610] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6852
pft 19 / 70
[2670] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6867
pft 23 / 123
[2730] +++++++++++++++++++++++++++++++++++++++++aaaaaaaaaaaaaaaaaaa 6877
pft 37 / 122
[2770] aaaaaapriv_ld addRead: 334719
priv_ld total: 373529
Timing BFC paf construct: 373580

ccon timings:
cct pre 2027
cct dir 3824
cct xcu 7819
cct tmp 1514
cct sw 203578
cct pic 1524
cct ico 92796
cct icm 0
cct upd 1691
cct del 0
cct rmz 1656
cct gcp 176

ccon i timings (2769):
ccit insglcc 177
ccit insglaro 651
ccit insglact 76
ccit insgltot 2786
ccit pr 17269
ccit templ 2423
ccit index 1473
ccit biglccins 3592
ccit biglinterpol 689
ccit biglupdtags 382
ccit biglfpcri 358
ccit bigllgap 14632
ccit biglshiftread 3087
ccit bigltot 38913
ccit insgr 1642
ccit ucv 14709

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2770
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:55 2015
Timing BFC analysereadcov: 12686
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 77
mict_fallout 6404
mict_newin 3726
mict_helper1 24045
mict_newin 3726
mict_restofloop 3810
mict_totalloop 52846
done.

-------------- Contig statistics ----------------
Contig id: 8
Contig length: 6877

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2770 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 149 0 0
0 0 0
Avg. coverage 0.000 0.000 75.313 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 149
Avg. contig coverage: 75.313

Consensus contains: A: 1030 C: 2036 G: 2094 T: 997 N: 0
IUPAC: 0 Funny: 0 *: 720
GC content: 67.078%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 53558
Localtime: Mon Jun 15 17:08:55 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 50210 cases.

P 1, marked 50210 reads.
Timing BFC edit tricky1: 32909
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 34168
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1084 cases.

Edited 1084 reads.
Localtime: Mon Jun 15 17:08:55 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:08:55 2015
Timing BFC edit tricky2: 25928

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 265 positions.
Localtime: Mon Jun 15 17:08:55 2015
Deleting superfluous gap columns (2) ... done, deleted 464 columns.
Localtime: Mon Jun 15 17:08:55 2015
Timing BFC edit single discrepancy, no HAF: 56014
bfc 12/0
Timing BFC delPSHP: 435
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 14140
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 378
mict_pre 7
mict_shadow 79
mict_fallout 5973
mict_newin 3499
mict_helper1 22219
mict_newin 3499
mict_restofloop 3558
mict_totalloop 49328
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 114732
Contig coverage analysis ... Timing BFC loop total: 720466
bfc 1
Localtime: Mon Jun 15 17:08:56 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 9
Localtime: Mon Jun 15 17:08:56 2015
Unused reads: 1657800
bfc 8/0
0 Known 1: 2770
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 521
pft 10 / 119
[61] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 602
pft 11 / 120
[120] +++++++++++++++++++++++++a++++++++++++++++++++++++++++++++++ 827
pft 12 / 114
[179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1015
pft 11 / 121
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1269
pft 9 / 125
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1319
pft 14 / 127
[359] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++a+ 1490
pft 14 / 125
[417] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1543
pft 17 / 115
[476] a++++++++++++++++++++++++++++++++++++++a+a++++++++++++++++++ 1609
pft 18 / 115
[534] ++++++++a+++++++++++++++++++++++++++++++++++++++++a+++++++++ 1641
pft 16 / 105
[592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1960
pft 12 / 118
[652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2062
pft 16 / 147
[712] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2122
pft 16 / 141
[771] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2169
pft 15 / 127
[831] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2203
pft 18 / 112
[890] +++++++++++++++++++++++++++++++++a+++++++a++++++++++++++++++ 2221
pft 18 / 101
[948] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2611
pft 12 / 110
[1007] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 2760
pft 11 / 124
[1065] a+++++++++++++++++++++++++++a+++++++++++++a+++++++++++++++++ 2836
pft 14 / 123
[1123] +++++++++++++++++++++a+++++++++++++++++++++++++++++a++++++++ 2867
pft 13 / 116
[1181] +++aa+++++a+++++++a+++++++++++++++++++++++++++++++++++++++++ 2919
pft 13 / 115
[1237] ++++++++++++++++++++a+a+++++++++++++++++++++++++++++++++++++ 3099
pft 16 / 97
[1295] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3201
pft 12 / 122
[1355] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3238
pft 16 / 137
[1415] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3553
pft 14 / 109
[1475] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3757
pft 13 / 124
[1535] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3803
pft 16 / 115
[1595] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3846
pft 18 / 106
[1655] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3896
pft 18 / 85
[1715] ++a+++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 3897
pft 19 / 92
[1773] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3946
pft 19 / 109
[1833] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4041
pft 19 / 136
[1893] +a++++++++++++++++++++++++++++++++++++d+++++++++++++++++++++ 4051
pft 9 / 139
[1951] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 4059
pft 27 / 146
[2010] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4066
pft 19 / 112
[2070] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4075
pft 30 / 152
[2130] ++++++++++++++G+G++G++++++++++++++++++++++++++++++++++++++++ 4089
pft 24 / 145
[2187] ++G+GG++++G+++++++++++++++++++++++++++++++++++++++++++G+GG+G 4111
pft 28 / 122
[2239] +GGGG+GGGG++GGG+G+GG+GGGGGGGGGGGG+G+GGGGGGGG+GGG+++G+GGGGGGG 4112
pft 10 / 110
[2252] GG+++++++++GGG++++++++++++++++++++++++++++++++++++++++++++++ 4813
pft 11 / 114
[2308] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5018
pft 11 / 121
[2368] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5179
pft 12 / 128
[2428] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5261
pft 13 / 139
[2488] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5327
pft 17 / 132
[2548] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5367
pft 18 / 133
[2608] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5544
pft 14 / 127
[2668] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5628
pft 11 / 127
[2728] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5755
pft 16 / 159
[2788] ++++++++a+++++a+a+a++++++++++++++++++++++a++++++++++++++++++ 5773
pft 16 / 128
[2843] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5786
pft 17 / 117
[2902] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5795
pft 17 / 113
[2962] +++++++++++++++++a++++++++++a++++++++++++++++++a++a+++++++++ 5875
pft 14 / 111
[3018] ++++++++++++++++++++++++++++++++++++++++++++++++++++a++++a++ 6003
pft 14 / 136
[3075] aa++++a++++++++a+++a++a++++++++++++++++++++++++a++++++++++++ 6011
pft 15 / 117
[3129] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6029
pft 25 / 139
[3189] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6037
pft 13 / 141
[3249] ++++++++++++++++++++++++++++++++a++++++++a++++++++++++++++++ 6044
pft 17 / 142
[3307] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6061
pft 22 / 152
[3367] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 6074
pft 43 / 148
[3426] +G+G+++G++G++G++G++++G+++G++++++++++++GGGG++++++++++++++++++ 6075
pft 12 / 133
[3474] ++++++++++++++++++++++++++++++++++++++++G+++G+++G++++++++++a 6083
pft 17 / 157
[3530] ++++++++++++G++G++++++++++++++++G++G+++G+G+G+++G+GG+++G+G+G+ 6094
pft 18 / 137
[3576] GGGGGG+++GGG+GGG+GG++++++G++++G++G+GGGGGG+GGGG+++GG++G+++G++ 6099
pft 16 / 117
[3606] ++G+GGG+++++++G+++++++GGG+++G+++GGG++G+GG++G+aG++G++G+G+GGGG 6100
pft 23 / 101
[3641] +++++GG+++G+++GGG++++G++a+GG++a+G+GG++G+GG+++GGG+++++aGGaG++ 6105
pft 24 / 101
[3676] +++++GG+G++G++++G+G++GGa++++G+GG+++a++++++++Ga+GGG+++++G+G++ 6107
pft 34 / 82
[3716] +++++G++++a++a+GGa++GGG+GGGGG+++aG+GG+Ga+G+aaaaaaaaaaaaaaaa+ 6109
pft 21 / 97
[3739] +aaa+aaaaaaaaaaaaaaaaaaaaaa+aa+aaaaaa+a++++GGGGGGGGGGGGGG+++ 6113
pft 6 / 97
[3750] G+++++G+G++++++G++++++GGGGGGGG++++++G+G+++G+GGGGGGGGG+GGGGGG 6113
pft 30 / 57
[3780] G++GG++++G++++++aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa++aaaaaaaaaa++ 6113
pft 158 / 99
[3797] +aaGGGaGGaaaaaG++++G++++++++++GGGGGGGGGGGGGGGG+GGGGGaGGGGGGG 6113
pft 21 / 142
[3812] GGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGaGGaGGGGG 6113
pft 9 / 84
[3812] GGGGGGGGaGGGGaGGGaaGGG+aGG+GGGGGaaaaaaaGGGGGGGGGGGGGGGGGGGGG 6113
pft 80 / 95
[3814] GGGGGGGGGGGGGGaaaaGGGGpriv_ld addRead: 541529
priv_ld total: 619254
Timing BFC paf construct: 619314

ccon timings:
cct pre 3197
cct dir 4759
cct xcu 17740
cct tmp 2282
cct sw 343676
cct pic 2082
cct ico 133588
cct icm 0
cct upd 2365
cct del 0
cct rmz 2287
cct gcp 1801

ccon i timings (3813):
ccit insglcc 348
ccit insglaro 1239
ccit insglact 159
ccit insgltot 4605
ccit pr 24955
ccit templ 3493
ccit index 1993
ccit biglccins 3705
ccit biglinterpol 720
ccit biglupdtags 421
ccit biglfpcri 387
ccit bigllgap 21247
ccit biglshiftread 4146
ccit bigltot 57258
ccit insgr 2096
ccit ucv 20703

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3814
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:56 2015
Timing BFC analysereadcov: 17342
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 119
mict_fallout 7245
mict_newin 3352
mict_helper1 31560
mict_newin 3352
mict_restofloop 3413
mict_totalloop 58854
done.

-------------- Contig statistics ----------------
Contig id: 9
Contig length: 6113

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3814 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 237 0 0
0 0 0
Avg. coverage 0.000 0.000 119.490 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 237
Avg. contig coverage: 119.490

Consensus contains: A: 1002 C: 1628 G: 1828 T: 878 N: 0
IUPAC: 0 Funny: 0 *: 777
GC content: 64.768%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 59789
Localtime: Mon Jun 15 17:08:56 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 80453 cases.

P 1, marked 80453 reads.
Timing BFC edit tricky1: 49233
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 50612
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 396 positions.
Localtime: Mon Jun 15 17:08:56 2015
Deleting superfluous gap columns (2) ... done, deleted 104 columns.
Localtime: Mon Jun 15 17:08:56 2015
Timing BFC edit single discrepancy, no HAF: 52670
bfc 12/0
Timing BFC delPSHP: 746
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: 320
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 251
mict_pre 7
mict_shadow 108
mict_fallout 7168
mict_newin 3333
mict_helper1 31656
mict_newin 3333
mict_restofloop 3344
mict_totalloop 58470
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 166953
Contig coverage analysis ... Timing BFC loop total: 1019381
bfc 1
Localtime: Mon Jun 15 17:08:57 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 10
Localtime: Mon Jun 15 17:08:57 2015
Unused reads: 1653986
bfc 8/0
0 Known 1: 3814
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 539
pft 11 / 112
[60] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 779
pft 10 / 120
[120] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 941
pft 11 / 122
[180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1093
pft 12 / 128
[240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1116
pft 16 / 133
[300] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 1181
pft 17 / 125
[359] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 1239
pft 18 / 117
[418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1585
pft 9 / 116
[478] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1688
pft 12 / 141
[538] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1761
pft 22 / 128
[598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1841
pft 17 / 104
[658] ++++++++++++++++++++++++a++++++++++++++++++a+++++++++a++++++ 1910
pft 17 / 100
[715] +++++a+++++++++++++++++++++a++++++++++++++++++++++++++++++++ 1946
pft 18 / 103
[773] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1969
pft 18 / 83
[833] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2023
pft 18 / 88
[892] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2312
pft 12 / 109
[952] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2428
pft 13 / 113
[1012] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2440
pft 13 / 113
[1072] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2463
pft 15 / 107
[1132] +++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 2510
pft 15 / 121
[1191] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2820
pft 12 / 119
[1251] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2989
pft 13 / 126
[1311] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3186
pft 15 / 152
[1371] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3243
pft 15 / 133
[1431] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3433
pft 12 / 124
[1491] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3725
pft 12 / 121
[1551] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3955
pft 12 / 127
[1611] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3998
pft 13 / 134
[1671] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4040
pft 18 / 134
[1731] +++a++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4073
pft 18 / 116
[1790] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4117
pft 18 / 113
[1850] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 4132
pft 19 / 116
[1909] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 4157
pft 19 / 110
[1968] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 4374
pft 15 / 100
[2027] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 4423
pft 15 / 122
[2086] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4499
pft 13 / 137
[2146] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4826
pft 12 / 108
[2206] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4968
pft 11 / 123
[2266] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 5041
pft 15 / 138
[2325] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5081
pft 14 / 118
[2385] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 5131
pft 13 / 116
[2444] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5494
pft 13 / 119
[2504] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5721
pft 10 / 128
[2564] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5801
pft 13 / 137
[2624] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5854
pft 16 / 133
[2684] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 5903
pft 19 / 119
[2743] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5946
pft 21 / 136
[2803] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5982
pft 18 / 111
[2863] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 6021
pft 12 / 157
[2922] +++++++++++++++++++++++++++a++++++++++++++++aa+++++aa+++++++ 6026
pft 10 / 131
[2977] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6428
pft 11 / 131
[3037] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6702
pft 9 / 128
[3097] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6933
pft 11 / 113
[3157] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6965
pft 14 / 117
[3217] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7007
pft 15 / 130
[3277] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7254
pft 12 / 118
[3337] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 7330
pft 15 / 113
[3396] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 7371
pft 17 / 116
[3455] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7402
pft 21 / 123
[3515] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7408
pft 18 / 88
[3575] +++++++++++++++++++aa+++++a+++++++++++++++++++++++++++++++++ 7667
pft 14 / 103
[3632] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7853
pft 10 / 118
[3692] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7915
pft 14 / 129
[3752] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7927
pft 18 / 121
[3811] d+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8112
pft 13 / 110
[3871] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8236
pft 14 / 122
[3931] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 8331
pft 12 / 129
[3990] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8435
pft 14 / 150
[4050] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 8442
pft 10 / 146
[4109] +++++++++++++++aa+++++++++++++++++++++++++++++++++++++++++++ 8451
pft 12 / 157
[4167] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8455
pft 17 / 169
[4226] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 8460
pft 19 / 151
[4285] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 8468
pft 21 / 160
[4344] ++++++++++++++++++++++++++++++++++++++aa++++++++++++++++++++ 8473
pft 25 / 141
[4402] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 8484
pft 25 / 149
[4461] ++++++a++++++++++++a+++++++++a++++++++++++++++++++++++++++++ 8494
pft 22 / 141
[4518] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 8499
pft 25 / 117
[4577] +++++a+++++++++a++++++++++++++++++++++++++++++++++++++++++++ 8501
pft 26 / 105
[4635] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 8506
pft 27 / 98
[4694] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8608
pft 21 / 131
[4754] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8770
pft 23 / 152
[4814] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9028
pft 11 / 123
[4874] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9146
pft 14 / 125
[4934] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9163
pft 16 / 132
[4994] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9253
pft 15 / 129
[5054] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9456
pft 9 / 138
[5114] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9527
pft 12 / 117
[5174] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9658
pft 12 / 122
[5234] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 10028
pft 14 / 104
[5293] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10304
pft 14 / 112
[5353] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10400
pft 12 / 130
[5412] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10752
pft 12 / 117
[5472] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10839
pft 15 / 136
[5532] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10955
pft 13 / 130
[5592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11266
pft 13 / 121
[5652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11646
pft 10 / 119
[5712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11824
pft 12 / 118
[5772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11869
pft 14 / 131
[5832] ++++++++++++++++++a+++++++++++++++++++++++++++++++a+++++++++ 11960
pft 16 / 142
[5890] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 12017
pft 14 / 138
[5949] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12026
pft 16 / 115
[6008] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 12037
pft 16 / 113
[6067] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 12147
pft 15 / 93
[6126] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12397
pft 9 / 120
[6186] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 12674
pft 10 / 136
[6245] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12839
pft 11 / 135
[6305] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12967
pft 13 / 130
[6365] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13020
pft 15 / 146
[6423] a+++++++++++++++a++++++++++a++++++++++++++++++++++++a+++++++ 13049
pft 20 / 108
[6480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13057
pft 20 / 86
[6540] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 13156
pft 18 / 72
[6599] +++++++++++++aa+++++++++++++++++++++++++++++++++++++++++++++ 13434
pft 14 / 119
[6657] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13508
pft 15 / 122
[6717] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13600
pft 15 / 119
[6777] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13663
pft 17 / 139
[6837] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13671
pft 10 / 133
[6897] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14090
pft 10 / 125
[6957] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14128
pft 16 / 146
[7017] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 14187
pft 14 / 125
[7076] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 14321
pft 12 / 125
[7135] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14328
pft 13 / 146
[7195] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14391
pft 15 / 145
[7255] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14408
pft 20 / 162
[7315] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 14422
pft 24 / 151
[7374] +++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++ 14430
pft 20 / 133
[7433] ++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++ 14444
pft 22 / 132
[7492] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 14679
pft 19 / 111
[7551] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14910
pft 11 / 117
[7611] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14971
pft 17 / 148
[7671] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14986
pft 19 / 126
[7731] ++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++ 14997
pft 18 / 118
[7790] +++++++++++++++++++a++++++++++++++++++++d+++++++++++++++++++ 15010
pft 15 / 133
[7848] +++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 15017
pft 18 / 126
[7907] +++++++++++++++++++++++++++++++++++++++++++++++++a+++++a++++ 15022
pft 16 / 145
[7965] ++++++++++++++++++++++++++++++++++++++a+++++++++++a+++++++++ 15028
pft 20 / 170
[8023] +++++++++++++++++++a++++++++a+++++++++++++++++++++++++++++++ 15033
pft 32 / 158
[8081] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 15042
pft 43 / 151
[8139] a++++++++++++++a++++++++++++++++++++++a+++++++++++++++++++++ 15051
pft 39 / 157
[8197] +++++G+++++++++++++++++++++++++++++++a+a++++a+++aG++++++++++ 15058
pft 26 / 182
[8251] +++a+++++++++++++++++a+++a+++a+++++a++a+a+++G+++++++++++a+++ 15070
pft 30 / 153
[8302] +a++++++++++++++G++++++++++++++a++++G++++++++++++G++++++++++ 15074
pft 26 / 100
[8357] +a+++++a+++++++aaaa++a++++++++++++++++++++++++++++++++++++++ 15075
pft 19 / 123
[8410] ++++++++++++G+++++++++++++++++++++++G+++a+++++++++G++a+++++G 15078
pft 12 / 153
[8464] +++G+++aa+G++GG++++GGGGG+a+GG++++aG+G+a+G++GGG+++GG++a+++++G 15081
pft 15 / 134
[8497] GGGGGGG+++GG++++GGG++GG++aa+a++a+++G+++G+aaaG++++++++a++aaaa 15081
pft 19 / 119
[8528] a++++aaG++G+a+G+G++++G+++aaGa+aa++aaG+++++aaaaaa++GGGG++++aG 15082
pft 23 / 110
[8558] G+++a++a+++GGGGGG++GGG++++G++GGa++GGGGGGG+++aaGG++GGGGGG++++ 15087
pft 24 / 89
[8586] ++aa+G++++++++a++GGGa+++aG++++G+++GGGGGG+GGG+aaa+aaaa++++G+a 15090
pft 33 / 85
[8616] aGGaa+G++Ga+aaaaaaaaaaaaa+++aa+GG+++++aa++G++++++++a+GaaGG++ 15098
pft 25 / 93
[8642] aaaaaa++G+aaaaaaaaaaaaaaaaaaaa+aaaaadaaaaaaaaa+aaaaa+aaaa+aa 15099
pft 165 / 123
[8650] +aaa+aaa+aGaaaaaaaGaaaaaaaaGaaaaaaaaaaaaaGaaaGGGGGGGGGGGaGaG 15099
pft 8 / 128
[8652] GGGaGaGGaaGGGaaGaGGG+GGaaGaaaGGGGGGGGGGGGGGGGaGGGGGaaGGGGGGG 15099
pft 5 / 104
[8653] GaGGaaaaaaaaaaaaaGaaaGaaaaaaaGGGGGGGaGG+GGaGGaGGGGGaaaaaaaaa 15099
pft 4 / 108
[8654] aaGGGGGGaGGGGaaaa+aaaaGGGGGGGGGGGGGaGGGGGGGGGGpriv_ld addRead: 1176416
priv_ld total: 1319703
Timing BFC paf construct: 1319779

ccon timings:
cct pre 6811
cct dir 11481
cct xcu 41924
cct tmp 4918
cct sw 722721
cct pic 4754
cct ico 312262
cct icm 0
cct upd 5475
cct del 0
cct rmz 5307
cct gcp 2068

ccon i timings (8654):
ccit insglcc 668
ccit insglaro 2150
ccit insglact 255
ccit insgltot 9173
ccit pr 59340
ccit templ 8736
ccit index 4720
ccit biglccins 11091
ccit biglinterpol 1773
ccit biglupdtags 1063
ccit biglfpcri 983
ccit bigllgap 51243
ccit biglshiftread 9456
ccit bigltot 135854
ccit insgr 4924
ccit ucv 47349

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 8655
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:08:58 2015
Timing BFC analysereadcov: 39525
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 268
mict_fallout 17090
mict_newin 8367
mict_helper1 74595
mict_newin 8367
mict_restofloop 8296
mict_totalloop 141299
done.

-------------- Contig statistics ----------------
Contig id: 10
Contig length: 15099

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 8655 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 212 0 0
0 0 0
Avg. coverage 0.000 0.000 109.991 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 212
Avg. contig coverage: 109.991

Consensus contains: A: 2368 C: 4250 G: 4251 T: 2342 N: 0
IUPAC: 0 Funny: 0 *: 1888
GC content: 64.348%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 143377
Localtime: Mon Jun 15 17:08:58 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 181596 cases.

P 1, marked 181596 reads.
Timing BFC edit tricky1: 114323
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 118425
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 967 positions.
Localtime: Mon Jun 15 17:08:58 2015
Deleting superfluous gap columns (2) ... done, deleted 275 columns.
Localtime: Mon Jun 15 17:08:58 2015
Timing BFC edit single discrepancy, no HAF: 129792
bfc 12/0
Timing BFC delPSHP: 2243
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: 624
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 856
mict_pre 7
mict_shadow 257
mict_fallout 16758
mict_newin 8186
mict_helper1 70288
mict_newin 8186
mict_restofloop 8178
mict_totalloop 135536
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 386743
Contig coverage analysis ... Timing BFC loop total: 2261535
bfc 1
Localtime: Mon Jun 15 17:08:59 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 11
Localtime: Mon Jun 15 17:08:59 2015
Unused reads: 1645331
bfc 8/0
0 Known 1: 8655
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 476
pft 11 / 118
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 626
pft 11 / 131
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 771
pft 16 / 146
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 797
pft 18 / 129
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 894
pft 15 / 125
[301] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 943
pft 20 / 119
[360] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 1156
pft 17 / 101
[419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1425
pft 11 / 117
[479] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1697
pft 11 / 123
[539] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1787
pft 13 / 135
[599] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1824
pft 16 / 131
[659] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1852
pft 17 / 129
[719] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1885
pft 19 / 119
[779] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++a+++++ 1926
pft 17 / 102
[837] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2214
pft 16 / 140
[897] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2245
pft 13 / 132
[957] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2290
pft 13 / 122
[1017] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2306
pft 17 / 106
[1077] ++++++++++++++++d+++++++++++++++++++++++++++++++++++a+++++++ 2413
pft 20 / 92
[1135] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2752
pft 13 / 113
[1195] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 2949
pft 10 / 117
[1254] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 3175
pft 12 / 116
[1313] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3317
pft 12 / 118
[1373] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3578
pft 11 / 117
[1433] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3658
pft 12 / 129
[1493] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3687
pft 14 / 138
[1553] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3793
pft 21 / 155
[1613] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 3826
pft 21 / 128
[1672] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3858
pft 18 / 108
[1732] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3869
pft 15 / 106
[1792] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 3916
pft 12 / 130
[1851] ++++++++++a++++++++++++++++++++++++++++++++++a++++++++++++++ 3928
pft 17 / 151
[1909] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3951
pft 10 / 147
[1969] +++a+++++++++++++++++++++++a++++++++++++++a+++++++++++++aa++ 3965
pft 11 / 151
[2024] ++++++++++++a+++++++++++++++++++++++++a+++++++++++++++++++++ 3971
pft 25 / 161
[2082] ++++++aa++++++++++++++++++a++++++++++++++a++++a+++++++++++++ 3982
pft 21 / 141
[2137] +++a+++++++++++++++++++++++++++++a+++++GGG+GG+++++++++++a+++ 3989
pft 19 / 111
[2189] +++++++++++++++++++++++++++++++++++++++++GGG+++G++G+G+GG+GGG 3997
pft 18 / 110
[2237] G+++++++++GGGGGGG++++G++G+++++++++++++++++++++++++++++++++++ 4301
pft 15 / 123
[2288] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 4553
pft 9 / 120
[2347] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4596
pft 14 / 140
[2407] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 4664
pft 17 / 95
[2466] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5011
pft 10 / 127
[2526] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5201
pft 11 / 131
[2586] ++++++++++++a++++++++++++a++++a+++++++++++++++++++++++++++++ 5304
pft 17 / 110
[2643] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5617
pft 16 / 88
[2703] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5759
pft 11 / 120
[2763] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5947
pft 16 / 129
[2823] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6157
pft 9 / 124
[2883] ++++++++a++++++++++++++a++++++++++++++++++++++++++++++++++++ 6301
pft 12 / 118
[2941] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6316
pft 21 / 118
[3001] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6509
pft 17 / 82
[3061] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6749
pft 10 / 119
[3121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7005
pft 11 / 130
[3181] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 7035
pft 18 / 106
[3240] +++++++a++++++++++++++++a+++++++++++++++++++++a+++++++++++++ 7043
pft 18 / 73
[3297] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 7546
pft 12 / 113
[3356] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 7911
pft 9 / 119
[3415] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8256
pft 10 / 118
[3475] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8287
pft 14 / 121
[3535] ++++++++++++++++++++++++++++++++++++++++++++++++a+++a+++++++ 8300
pft 18 / 99
[3593] +++++++a+++++++++a+++++++++++++++++++++++++++a++++++++++a+++ 8312
pft 18 / 83
[3649] +++aa+++++++++++++++++++a+++++++++++++++a+++++a+++++++++++++ 8321
pft 16 / 68
[3704] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8755
pft 11 / 93
[3764] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9236
pft 12 / 138
[3824] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9355
pft 10 / 128
[3884] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9696
pft 12 / 124
[3944] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9743
pft 13 / 128
[4004] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 9889
pft 12 / 125
[4063] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9976
pft 12 / 136
[4123] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10065
pft 15 / 131
[4183] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10081
pft 11 / 140
[4243] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10083
pft 14 / 124
[4303] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 10086
pft 14 / 118
[4362] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10449
pft 11 / 117
[4422] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10580
pft 13 / 135
[4482] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10674
pft 17 / 144
[4541] ++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 10732
pft 19 / 130
[4600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10765
pft 19 / 107
[4660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10807
pft 17 / 108
[4720] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10823
pft 18 / 131
[4780] ++++a++++++++a+++++++++++++++++++++++++++++++++a++++++++++++ 10933
pft 10 / 138
[4837] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11196
pft 11 / 126
[4897] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11268
pft 14 / 126
[4957] +++++++++++++++++++++++++++++++++++aaaa+++++++++++++++++++++ 11447
pft 12 / 103
[5013] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11973
pft 10 / 115
[5073] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12152
pft 11 / 123
[5133] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12452
pft 12 / 127
[5193] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12575
pft 14 / 148
[5253] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12702
pft 12 / 139
[5313] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12829
pft 18 / 129
[5373] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 12973
pft 10 / 121
[5432] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 13080
pft 18 / 128
[5491] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13089
pft 19 / 96
[5550] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 13098
pft 21 / 86
[5609] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13432
pft 16 / 96
[5669] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13767
pft 9 / 125
[5729] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14038
pft 10 / 119
[5789] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 14147
pft 10 / 122
[5848] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14241
pft 17 / 127
[5908] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14285
pft 21 / 128
[5968] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14619
pft 14 / 111
[6028] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14748
pft 10 / 109
[6088] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14753
pft 16 / 93
[6148] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14765
pft 19 / 90
[6208] +++++++++++++++++++++++a++aaaa++++++++++++++++++++++++++++++ 14777
pft 15 / 163
[6263] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14779
pft 27 / 142
[6323] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14793
pft 30 / 150
[6383] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 14801
pft 33 / 125
[6442] ++++++++++++++++++++a+++++++++++++a+++++++++++++++++++++++++ 14809
pft 30 / 161
[6500] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15060
pft 26 / 113
[6559] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15261
pft 11 / 126
[6619] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15359
pft 17 / 140
[6679] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15369
pft 16 / 123
[6739] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 15388
pft 15 / 126
[6798] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15392
pft 18 / 150
[6858] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15400
pft 40 / 132
[6918] +a++++++aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaa+a++aaaaa+a++aaaaa 15402
pft 81 / 105
[6931] aaa++aaa+aaa+a++aaa+++aaaaaa+aaa+aaa+a++++++++aa+aapriv_ld addRead:
888071
priv_ld total: 988323
Timing BFC paf construct: 988411

ccon timings:
cct pre 5193
cct dir 6927
cct xcu 28022
cct tmp 3793
cct sw 538074
cct pic 3762
cct ico 247253
cct icm 0
cct upd 4381
cct del 0
cct rmz 4240
cct gcp 621

ccon i timings (6951):
ccit insglcc 1034
ccit insglaro 3448
ccit insglact 431
ccit insgltot 10633
ccit pr 47072
ccit templ 6726
ccit index 3770
ccit biglccins 8171
ccit biglinterpol 1606
ccit biglupdtags 920
ccit biglfpcri 825
ccit bigllgap 38289
ccit biglshiftread 9605
ccit bigltot 103661
ccit insgr 3765
ccit ucv 37587

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 6952
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:00 2015
Timing BFC analysereadcov: 32423
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 11
mict_shadow 327
mict_fallout 15260
mict_newin 8437
mict_helper1 59248
mict_newin 8437
mict_restofloop 8602
mict_totalloop 124857
done.

-------------- Contig statistics ----------------
Contig id: 11
Contig length: 15404

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 6952 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 183 0 0
0 0 0
Avg. coverage 0.000 0.000 86.082 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 183
Avg. contig coverage: 86.082

Consensus contains: A: 2293 C: 4501 G: 4552 T: 2375 N: 0
IUPAC: 0 Funny: 0 *: 1683
GC content: 65.979%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 127223
Localtime: Mon Jun 15 17:09:00 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 135064 cases.

P 1, marked 135064 reads.
Timing BFC edit tricky1: 90678
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 90355
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 2449 cases.

Edited 2449 reads.
Localtime: Mon Jun 15 17:09:00 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:00 2015
Timing BFC edit tricky2: 64466

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 633 positions.
Localtime: Mon Jun 15 17:09:00 2015
Deleting superfluous gap columns (2) ... done, deleted 1020 columns.
Localtime: Mon Jun 15 17:09:00 2015
Timing BFC edit single discrepancy, no HAF: 149464
bfc 12/0
Timing BFC delPSHP: 1683
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 38536
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 877
mict_pre 7
mict_shadow 215
mict_fallout 14089
mict_newin 7756
mict_helper1 54224
mict_newin 7756
mict_restofloop 7922
mict_totalloop 114921
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 292751
Contig coverage analysis ... Timing BFC loop total: 1883299
bfc 1
Localtime: Mon Jun 15 17:09:01 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 12
Localtime: Mon Jun 15 17:09:01 2015
Unused reads: 1638379
bfc 8/0
0 Known 1: 6952
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 501
pft 13 / 117
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 596
pft 13 / 133
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 882
pft 14 / 117
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1035
pft 14 / 126
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1129
pft 16 / 135
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1195
pft 18 / 131
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1231
pft 14 / 120
[421] +++++++++++++++++++++++++++++++++++++++a++d+++a++++++++++++a 1271
pft 14 / 112
[477] +++++++++++++++++a+++++a+++++++a++++++++++++++++++++++++++++ 1513
pft 13 / 104
[534] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1802
pft 9 / 111
[594] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2093
pft 11 / 121
[654] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2190
pft 15 / 121
[714] +++++++++++a+++++++++++++++++++++++++++++++++++++++a++++++++ 2195
pft 18 / 98
[772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2387
pft 15 / 115
[832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2532
pft 12 / 127
[892] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2584
pft 14 / 122
[952] +++++++++++a+++++++++++++++++++++++++++++a++++++++++++++++++ 2596
pft 14 / 122
[1010] ++++++++a+++++a++a++++++++++++++++a+++++++++++++++++++++++++ 2623
pft 16 / 141
[1066] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 2889
pft 13 / 113
[1125] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2906
pft 11 / 129
[1185] ++++++++++a+++++++a++++++a++++++++++++++++a++a++++++a+++++++ 2917
pft 12 / 127
[1239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3302
pft 15 / 122
[1299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3534
pft 11 / 122
[1359] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3688
pft 9 / 121
[1419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3769
pft 12 / 129
[1479] ++++++++++++++++++++++++++++a++++++++++++++++++++++a+a++++++ 3813
pft 18 / 110
[1536] +++++++++++++++++++++++++a+a++++++++++++++++++++++++++++++++ 3864
pft 18 / 102
[1594] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4190
pft 13 / 109
[1654] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4241
pft 12 / 144
[1714] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4283
pft 14 / 152
[1774] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4341
pft 17 / 143
[1834] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4591
pft 13 / 117
[1894] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4639
pft 13 / 120
[1954] +++a++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 4890
pft 11 / 108
[2012] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5177
pft 13 / 113
[2072] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5284
pft 14 / 124
[2132] +++++++++++++++++++++++++++++a+++++++++++++++++++++a++++++++ 5296
pft 17 / 94
[2190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5731
pft 12 / 104
[2250] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5893
pft 11 / 120
[2310] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6200
pft 11 / 117
[2370] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6240
pft 14 / 125
[2430] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6339
pft 18 / 121
[2490] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6368
pft 23 / 124
[2550] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6375
pft 21 / 78
[2610] +++++++++++++++++++++++++++++++++++++++++++aa+++++++++++++++ 6380
pft 20 / 95
[2668] ++aa+++++a++++aa++++++++++++++++++++++a+++++aa++++++a+++++++ 6386
pft 10 / 144
[2718] a+++a+++++a++a+++++a+aa+++a+++++++++++a+a+++++++++++aa+aaaaa 6424
pft 8 / 122
[2762] ++++++++++++++++++a+++++++++a++++++a+++++++++++++++++++a++++ 6428
pft 18 / 160
[2818] +++a+a+++++++++++++++++++++a+a+a++++++++++++++++++a+++aa++++ 6439
pft 21 / 160
[2869] a++++++a++++++a+++++a++++a+++++++++++++++++++aa+++++++++aa++ 6452
pft 26 / 148
[2921] +++++++++++d+++++++++++++++++++a++++++++++++++++++++++++++++ 6457
pft 27 / 110
[2979] +++++++++++a+a++++++++++++++++++++++++++++++++++++++++++++++ 6461
pft 32 / 91
[3036] aaaaa+aaa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa++aaaa 6461
pft 30 / 112
[3040] aaaapriv_ld addRead: 392648
priv_ld total: 438262
Timing BFC paf construct: 438332

ccon timings:
cct pre 2289
cct dir 3903
cct xcu 13532
cct tmp 1737
cct sw 241704
cct pic 1652
cct ico 103280
cct icm 0
cct upd 1883
cct del 0
cct rmz 1826
cct gcp 560

ccon i timings (3039):
ccit insglcc 136
ccit insglaro 438
ccit insglact 50
ccit insgltot 2585
ccit pr 18845
ccit templ 2679
ccit index 1623
ccit biglccins 3489
ccit biglinterpol 674
ccit biglupdtags 367
ccit biglfpcri 339
ccit bigllgap 16612
ccit biglshiftread 3057
ccit bigltot 44437
ccit insgr 1792
ccit ucv 16502

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3040
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:01 2015
Timing BFC analysereadcov: 14976
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 10
mict_shadow 108
mict_fallout 6427
mict_newin 3422
mict_helper1 25194
mict_newin 3422
mict_restofloop 3491
mict_totalloop 52316
done.

-------------- Contig statistics ----------------
Contig id: 12
Contig length: 6461

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3040 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 168 0 0
0 0 0
Avg. coverage 0.000 0.000 89.367 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 168
Avg. contig coverage: 89.367

Consensus contains: A: 1030 C: 1823 G: 1934 T: 971 N: 0
IUPAC: 0 Funny: 0 *: 703
GC content: 65.248%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 53016
Localtime: Mon Jun 15 17:09:01 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 59302 cases.

P 1, marked 59302 reads.
Timing BFC edit tricky1: 36858
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 40511
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1076 cases.

Edited 1076 reads.
Localtime: Mon Jun 15 17:09:01 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:01 2015
Timing BFC edit tricky2: 26655

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 284 positions.
Localtime: Mon Jun 15 17:09:01 2015
Deleting superfluous gap columns (2) ... done, deleted 432 columns.
Localtime: Mon Jun 15 17:09:01 2015
Timing BFC edit single discrepancy, no HAF: 62835
bfc 12/0
Timing BFC delPSHP: 591
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 16942
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 385
mict_pre 5
mict_shadow 91
mict_fallout 5924
mict_newin 3174
mict_helper1 23496
mict_newin 3174
mict_restofloop 3181
mict_totalloop 48863
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 124222
Contig coverage analysis ... Timing BFC loop total: 817424
bfc 1
Localtime: Mon Jun 15 17:09:02 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 13
Localtime: Mon Jun 15 17:09:02 2015
Unused reads: 1635339
bfc 8/0
0 Known 1: 3040
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 407
pft 12 / 120
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 595
pft 10 / 129
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 691
pft 12 / 125
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 829
pft 21 / 147
[241] +++++++++++++++++++++++++++a+++a+++++++++++++++++++++++a+a++ 999
pft 20 / 114
[297] +++a+++++++a++a+++++++++++++++++++++++++++++++++++++++++++++ 1033
pft 16 / 113
[354] ++++a++++++++a++++++++++++++++++++++++++++++++++++++d+++++++ 1090
pft 16 / 104
[411] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1371
pft 11 / 111
[471] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1592
pft 9 / 128
[531] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1843
pft 10 / 126
[591] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1861
pft 13 / 138
[651] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1892
pft 19 / 126
[711] +++++++++++++++++++++++++++++++a++++++++++++++++a+++++++++++ 1905
pft 22 / 93
[769] ++++++++++++++++++++++a++++++++++++++++++++++++++a++++++++++ 1962
pft 15 / 106
[827] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++a+ 2205
pft 10 / 105
[885] ++++++++++++++++++++++++++++++++++++a+++++++++a+++++++++++++ 2207
pft 14 / 149
[943] ++++a++++++++++++++++++a+d+++a+++++++++aa++++++a+++++++++++a 2215
pft 26 / 108
[995] ++aaaa+aaadaaaaaaa++aa+adaaaapriv_ld addRead: 128130
priv_ld total: 143322
Timing BFC paf construct: 143387

ccon timings:
cct pre 749
cct dir 945
cct xcu 4184
cct tmp 575
cct sw 79295
cct pic 546
cct ico 33808
cct icm 0
cct upd 646
cct del 0
cct rmz 617
cct gcp 175

ccon i timings (999):
ccit insglcc 124
ccit insglaro 433
ccit insglact 51
ccit insgltot 1389
ccit pr 6093
ccit templ 793
ccit index 564
ccit biglccins 732
ccit biglinterpol 215
ccit biglupdtags 131
ccit biglfpcri 126
ccit bigllgap 5182
ccit biglshiftread 1115
ccit bigltot 14196
ccit insgr 548
ccit ucv 5368

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1000
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:02 2015
Timing BFC analysereadcov: 4461
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 28
mict_fallout 2128
mict_newin 1243
mict_helper1 8204
mict_newin 1243
mict_restofloop 1159
mict_totalloop 17422
done.

-------------- Contig statistics ----------------
Contig id: 13
Contig length: 2215

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1000 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 161 0 0
0 0 0
Avg. coverage 0.000 0.000 85.160 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 161
Avg. contig coverage: 85.160

Consensus contains: A: 355 C: 617 G: 634 T: 366 N: 0
IUPAC: 0 Funny: 0 *: 243
GC content: 63.438%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 17656
Localtime: Mon Jun 15 17:09:02 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 20789 cases.

P 1, marked 20789 reads.
Timing BFC edit tricky1: 11929
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 12844
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 390 cases.

Edited 390 reads.
Localtime: Mon Jun 15 17:09:02 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:02 2015
Timing BFC edit tricky2: 9565

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 93 positions.
Localtime: Mon Jun 15 17:09:02 2015
Deleting superfluous gap columns (2) ... done, deleted 136 columns.
Localtime: Mon Jun 15 17:09:02 2015
Timing BFC edit single discrepancy, no HAF: 18790
bfc 12/0
Timing BFC delPSHP: 134
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 5263
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 90
mict_pre 5
mict_shadow 29
mict_fallout 2170
mict_newin 1140
mict_helper1 8362
mict_newin 1140
mict_restofloop 1195
mict_totalloop 17580
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 40594
Timing BFC loop total: 265274
bfc 1
Localtime: Mon Jun 15 17:09:02 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 14
Localtime: Mon Jun 15 17:09:02 2015
Unused reads: 1634339
bfc 8/0
0 Known 1: 1000
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 419
pft 12 / 119
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 483
pft 13 / 126
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 791
pft 11 / 117
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 959
pft 10 / 121
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1032
pft 15 / 127
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1218
pft 13 / 124
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1533
pft 10 / 121
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1623
pft 13 / 151
[481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1782
pft 14 / 126
[541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1810
pft 20 / 130
[601] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 1850
pft 20 / 105
[660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1866
pft 16 / 104
[720] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2152
pft 14 / 102
[780] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2378
pft 10 / 119
[840] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2593
pft 9 / 119
[900] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2665
pft 11 / 130
[960] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2744
pft 15 / 110
[1020] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2773
pft 14 / 110
[1080] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3058
pft 10 / 124
[1140] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 3143
pft 13 / 126
[1199] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 3437
pft 20 / 98
[1258] +++++++++++a+++++++++++++++++++a++++++++++++a+++++++++++++++ 3462
pft 15 / 133
[1315] ++++++++++++++++++++aa++++++a++++++++++++++++++++++++++++++a 3467
pft 12 / 150
[1371] ++++++++++++++a++d++++++++++a+++++++++++++++++++++++++++++++ 3477
pft 31 / 137
[1428] ++++++++++++++++++++++++++++++aaaaaaaaaa+daaaaaaaaaaa+aaaaaa 3480
pft 15 / 88
[1459] aaa+++++++aaaaaaadaaaaaaapriv_ld addRead: 188306
priv_ld total: 208432
Timing BFC paf construct: 208486

ccon timings:
cct pre 1095
cct dir 1547
cct xcu 6157
cct tmp 813
cct sw 116103
cct pic 783
cct ico 49918
cct icm 0
cct upd 933
cct del 0
cct rmz 920
cct gcp 191

ccon i timings (1465):
ccit insglcc 163
ccit insglaro 625
ccit insglact 71
ccit insgltot 2073
ccit pr 9131
ccit templ 1190
ccit index 810
ccit biglccins 1500
ccit biglinterpol 322
ccit biglupdtags 195
ccit biglfpcri 179
ccit bigllgap 7980
ccit biglshiftread 1701
ccit bigltot 20824
ccit insgr 840
ccit ucv 7973

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1466
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:02 2015
Timing BFC analysereadcov: 6690
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 6
mict_shadow 44
mict_fallout 3276
mict_newin 1785
mict_helper1 12270
mict_newin 1785
mict_restofloop 1897
mict_totalloop 26802
done.

-------------- Contig statistics ----------------
Contig id: 14
Contig length: 3483

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1466 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 168 0 0
0 0 0
Avg. coverage 0.000 0.000 80.989 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 168
Avg. contig coverage: 80.989

Consensus contains: A: 579 C: 1059 G: 1005 T: 489 N: 0
IUPAC: 0 Funny: 0 *: 351
GC content: 65.900%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 27132
Localtime: Mon Jun 15 17:09:02 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 27609 cases.

P 1, marked 27609 reads.
Timing BFC edit tricky1: 17177
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 21033
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 165 positions.
Localtime: Mon Jun 15 17:09:02 2015
Deleting superfluous gap columns (2) ... done, deleted 69 columns.
Localtime: Mon Jun 15 17:09:02 2015
Timing BFC edit single discrepancy, no HAF: 20091
bfc 12/0
Timing BFC delPSHP: 170
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: 123
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 111
mict_pre 6
mict_shadow 41
mict_fallout 3246
mict_newin 1804
mict_helper1 11820
mict_newin 1804
mict_restofloop 1875
mict_totalloop 26043
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 65482
Timing BFC loop total: 367369
bfc 1
Localtime: Mon Jun 15 17:09:02 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 15
Localtime: Mon Jun 15 17:09:02 2015
Unused reads: 1632873
bfc 8/0
0 Known 1: 1466
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 546
pft 12 / 112
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 608
pft 13 / 126
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 848
pft 11 / 123
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 927
pft 12 / 124
[241] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 971
pft 12 / 120
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1316
pft 12 / 112
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1545
pft 11 / 115
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1599
pft 13 / 128
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1638
pft 18 / 125
[540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1737
pft 20 / 132
[600] ++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 2004
pft 12 / 121
[659] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 2064
pft 12 / 134
[718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 2121
pft 15 / 133
[776] a+++++++++++++++++a+++++++++a++a++a+++a+++++++a+a++++++++a++ 2127
pft 17 / 101
[828] ++++++++++++++++a++++++++++++++++a+++++++++++++++++++++a++a+ 2180
pft 18 / 95
[884] ++++++++++++a+++++++++++++++++++++++++++++++++++++aa++++a+++ 2186
pft 16 / 97
[940] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 2260
pft 15 / 105
[999] ++++++++++++++++++++++++++a+aa++++++++++++++++++++++++++++++ 2273
pft 14 / 105
[1056] +++++++++a+++++++++++++++++++++++++++++++++a++++++++++++++++ 2512
pft 13 / 110
[1114] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 2551
pft 15 / 148
[1173] ++++++++++++++++++++++++++++++a++++++++++++++a++++++++++++++ 2595
pft 9 / 141
[1231] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 2810
pft 11 / 120
[1290] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3093
pft 11 / 123
[1350] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3137
pft 15 / 118
[1410] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3241
pft 17 / 125
[1470] +++++++++++++++++++++++++++++a+++++a++++++++++++++++++++++++ 3412
pft 15 / 122
[1528] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3521
pft 10 / 114
[1588] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3533
pft 15 / 148
[1648] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3541
pft 21 / 155
[1708] ++++++++++++++++++++++++++++++++++++a++++a++++++++++++++++++ 3550
pft 27 / 139
[1766] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 3560
pft 20 / 126
[1825] ++++++++++++++++++++++++++++++++++++++++++++++++++GGGGG+G+++ 3566
pft 15 / 107
[1879] +++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++ 3573
pft 16 / 106
[1938] ++++++++G+++++++G+++++++G++++GGG+++++++G+G++++++++++++++a+++ 3580
pft 14 / 104
[1989] +++++++++++++++++++++G+++G++GGGG+GG+++++++++G+G+GGGG+GG+++++ 3586
pft 9 / 117
[2032] Ga+++G+++++++GG++++G+G++++G++GG++G+++GGa+G+++++G++G+++++++++ 3958
pft 19 / 106
[2076] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4134
pft 11 / 127
[2136] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4343
pft 9 / 130
[2196] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4421
pft 12 / 131
[2256] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 4467
pft 11 / 129
[2315] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4733
pft 11 / 124
[2375] ++++++++++++++a++++++++++++++++a+++++++++++a++++++++++++++++ 4984
pft 9 / 127
[2432] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4995
pft 10 / 132
[2492] +++++++++++++a+++++++++++a++++a++++++++++++++++++++a++++++++ 5004
pft 11 / 149
[2548] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5016
pft 11 / 151
[2608] +++++++a+++++++++++++++++++a++++++++++++++++++++++++++++++++ 5025
pft 14 / 155
[2666] +++++++++++++++++++++++++++a+++++a++++++++++++++++++++++++++ 5032
pft 18 / 143
[2724] +++++++++++++a+++++++++++a++++++++++++++++++++a+++++++++++++ 5048
pft 19 / 166
[2781] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 5061
pft 17 / 149
[2840] ++++++++++++++++++++++a++++++d++++++++++++++++++++++++++++++ 5068
pft 14 / 132
[2898] +++++++++++++++++++++d++++++++++++++++++++++++G+++++++++++++ 5076
pft 13 / 130
[2956] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 5083
pft 13 / 160
[3015] ++++++++++++++++++G+++++G+++++++++++++++++++++++++++++++++++ 5086
pft 23 / 139
[3073] +++++++++++++++++++++++++++++++++++a+++++++++++++++++a++a+++ 5100
pft 39 / 159
[3130] ++++++++++++++++++++++++G++++++++++++++G++++++++++++++++++++ 5109
pft 21 / 133
[3188] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5119
pft 33 / 145
[3248] ++++++++++++++++++a+++++++++++++++aGG++G++GG++G+GGGGGG+G+++G 5119
pft 24 / 98
[3291] GGGG+G+G+GGGGGGGGGGG++G++++GG+++GG+++G++GG+Ga++++G+GGGGG+G++ 5124
pft 19 / 111
[3318] +GG+++++GG++G+G+G+G+G+GG+G+++++GGGGG+G+G++G+++++++GGGGGGGGGG 5130
pft 33 / 110
[3347] GGGGaGG+G+++GG++G++GGGG+++GGG++++++++GGGGGGG+G+++++++GGGGGGG 5131
pft 30 / 72
[3374] GGGGG+++GGGGGGGGGGGG+GG++G+GGGGGGGGGG+GGG+G+G+GGGGGGGGGGGGG+ 5131
pft 10 / 55
[3386] GG++G++G+GGGGGGGGGGGG+G+G+GG+G+GGGGGG+Gaaaaaa+aaaaaaaa+aaa+a 5134
pft 136 / 72
[3401] +++aa+aaaaaaaaaaaa++a++++++aaaa+++G+GGG++++++GG+GGaaGaaa++++ 5137
pft 11 / 150
[3427] GG+++++++++a++GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5138
pft 34 / 118
[3438] GGGGGGGGGGGGGGGGGGaaaaGGGGGaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5138
pft 6 / 75
[3438] GaaaaaaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 494352
priv_ld total: 559089
Timing BFC paf construct: 559144

ccon timings:
cct pre 2894
cct dir 5625
cct xcu 22563
cct tmp 2044
cct sw 309663
cct pic 1902
cct ico 119245
cct icm 0
cct upd 2205
cct del 0
cct rmz 2057
cct gcp 1447

ccon i timings (3437):
ccit insglcc 29
ccit insglaro 92
ccit insglact 10
ccit insgltot 2124
ccit pr 21435
ccit templ 3117
ccit index 1818
ccit biglccins 3830
ccit biglinterpol 642
ccit biglupdtags 366
ccit biglfpcri 372
ccit bigllgap 20191
ccit biglshiftread 2813
ccit bigltot 53202
ccit insgr 1967
ccit ucv 18801

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3438
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:03 2015
Timing BFC analysereadcov: 15568
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 10
mict_shadow 114
mict_fallout 6491
mict_newin 2845
mict_helper1 29030
mict_newin 2845
mict_restofloop 2874
mict_totalloop 52351
done.

-------------- Contig statistics ----------------
Contig id: 15
Contig length: 5138

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3438 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 215 0 0
0 0 0
Avg. coverage 0.000 0.000 129.732 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 215
Avg. contig coverage: 129.732

Consensus contains: A: 865 C: 1326 G: 1488 T: 763 N: 0
IUPAC: 0 Funny: 0 *: 696
GC content: 63.350%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 53010
Localtime: Mon Jun 15 17:09:03 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 73976 cases.

P 1, marked 73976 reads.
Timing BFC edit tricky1: 44526
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 48077
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 306 positions.
Localtime: Mon Jun 15 17:09:03 2015
Deleting superfluous gap columns (2) ... done, deleted 82 columns.
Localtime: Mon Jun 15 17:09:03 2015
Timing BFC edit single discrepancy, no HAF: 46178
bfc 12/0
Timing BFC delPSHP: 625
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: 283
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 197
mict_pre 15
mict_shadow 104
mict_fallout 6446
mict_newin 2779
mict_helper1 28778
mict_newin 2779
mict_restofloop 2832
mict_totalloop 51943
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 154914
Contig coverage analysis ... Timing BFC loop total: 924734
bfc 1
Localtime: Mon Jun 15 17:09:03 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 16
Localtime: Mon Jun 15 17:09:03 2015
Unused reads: 1629435
bfc 8/0
0 Known 1: 3438
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 443
pft 11 / 123
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 550
pft 13 / 139
[121] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 792
pft 13 / 118
[180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1069
pft 11 / 114
[240] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 1235
pft 12 / 116
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1353
pft 11 / 121
[359] +++a++++++++++++++++++++++++++++a+++++++++++++++++++++a+++a+ 1492
pft 13 / 127
[415] ++++++++++++++++++++++++++++++++++++++++++++++a++++++a++++++ 1600
pft 15 / 131
[473] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1881
pft 12 / 117
[533] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2008
pft 15 / 143
[593] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2080
pft 14 / 139
[653] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 2093
pft 18 / 121
[712] ++a++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 2110
pft 25 / 114
[770] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2132
pft 20 / 101
[830] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 2149
pft 21 / 86
[889] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2319
pft 22 / 84
[949] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2538
pft 10 / 120
[1009] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2559
pft 14 / 126
[1069] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2566
pft 16 / 99
[1129] +++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++a 2587
pft 20 / 78
[1187] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2887
pft 14 / 111
[1247] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 3048
pft 10 / 135
[1306] ++++++++++++++++++++++++a+++a+++++++++a+++++++++aa++++++++++ 3272
pft 21 / 123
[1361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3423
pft 12 / 114
[1421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3697
pft 14 / 109
[1481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3765
pft 12 / 127
[1541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3837
pft 11 / 131
[1601] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4160
pft 11 / 118
[1661] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 4242
pft 13 / 114
[1720] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4295
pft 14 / 113
[1780] ++++++++++++++++++++++++++++a++a+aaa+a+++++++++++++a++++++++ 4319
pft 11 / 125
[1833] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 4903
pft 8 / 105
[1892] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5187
pft 9 / 106
[1952] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5200
pft 17 / 75
[2012] +++++++++++++++++++++++++a+++++a++++++++++++++++++++++++++++ 5212
pft 16 / 118
[2070] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 5225
pft 12 / 172
[2129] +++++++++++++++++++++++++++a++++++++++++++a+a++++++++a++++++ 5228
pft 21 / 144
[2185] ++++++++++++++++++++++++++++++++++++++++++++++a++++++++++++G 5238
pft 17 / 116
[2243] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 5241
pft 19 / 152
[2302] +++++++++++++++++++++++++a+++d+++++++++++++++a+GG+GGa+a+a+++ 5261
pft 30 / 127
[2352] ++++++++aa+a+++++++a++++++++a++++++++a++++++++++++++++++++++ 5457
pft 14 / 123
[2406] ++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++ 5514
pft 11 / 140
[2465] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5752
pft 11 / 133
[2525] ++a+++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 5829
pft 11 / 138
[2583] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 5839
pft 10 / 147
[2642] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5847
pft 12 / 148
[2702] ++++++++++++++++++++++++++++++++++++++++++++++++G+++GG+G+G++ 5854
pft 26 / 160
[2757] +G+G+++++++++++++++++++++++++++++++++++++++a+++a++++++aa++++ 5872
pft 30 / 125
[2811] +++++++++++++++++++++++++G++GG+G++++G+++G++G+GGG++aG+GG+Ga++ 5877
pft 13 / 143
[2855] +G+GG+GG+G++G+G++G+G+G+G+G+G+a++++++G+G+GG+++G+++G++++a+++++ 5883
pft 34 / 107
[2893] +++GG+G+++++GG+GGGGGGGGGGG+++++GG+++G+GG++GGGGGGGGGGGGGGGGGG 5883
pft 28 / 67
[2913] GG++++GG++GGGGGGGGG++GGGGG+G+aaaaaaaaaaaaaa+aaaaaa+aaaaaa+G+ 5885
pft 82 / 96
[2928] +++aaaaGGGaa+Gaaaaaa+GGG+GGGaGGaGGGGGGGGaaGGGaGGGaaGGGGGGGG+ 5885
pft 16 / 111
[2934] GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGaGGaGGGGaaaGaaGGGGGGGGGGGGGGG 5885
pft 52 / 83
[2934] GGGGGGGGGGpriv_ld addRead: 397197
priv_ld total: 448223
Timing BFC paf construct: 448296

ccon timings:
cct pre 2297
cct dir 3318
cct xcu 14447
cct tmp 1703
cct sw 247923
cct pic 1657
cct ico 101108
cct icm 0
cct upd 1857
cct del 0
cct rmz 1762
cct gcp 769

ccon i timings (2933):
ccit insglcc 265
ccit insglaro 942
ccit insglact 117
ccit insgltot 3462
ccit pr 18627
ccit templ 2527
ccit index 1613
ccit biglccins 2476
ccit biglinterpol 616
ccit biglupdtags 367
ccit biglfpcri 319
ccit bigllgap 15981
ccit biglshiftread 3340
ccit bigltot 43122
ccit insgr 1638
ccit ucv 15750

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2934
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:04 2015
Timing BFC analysereadcov: 13375
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 93
mict_fallout 6181
mict_newin 3178
mict_helper1 25324
mict_newin 3178
mict_restofloop 3241
mict_totalloop 50808
done.

-------------- Contig statistics ----------------
Contig id: 16
Contig length: 5885

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2934 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 207 0 0
0 0 0
Avg. coverage 0.000 0.000 94.863 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 207
Avg. contig coverage: 94.863

Consensus contains: A: 855 C: 1714 G: 1716 T: 937 N: 0
IUPAC: 0 Funny: 0 *: 663
GC content: 65.684%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 51513
Localtime: Mon Jun 15 17:09:04 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 61363 cases.

P 1, marked 61363 reads.
Timing BFC edit tricky1: 36445
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 38253
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1020 cases.

Edited 1020 reads.
Localtime: Mon Jun 15 17:09:04 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:04 2015
Timing BFC edit tricky2: 26587

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 272 positions.
Localtime: Mon Jun 15 17:09:04 2015
Deleting superfluous gap columns (2) ... done, deleted 401 columns.
Localtime: Mon Jun 15 17:09:04 2015
Timing BFC edit single discrepancy, no HAF: 59548
bfc 12/0
Timing BFC delPSHP: 593
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 18369
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 362
mict_pre 6
mict_shadow 91
mict_fallout 5575
mict_newin 2876
mict_helper1 22358
mict_newin 2876
mict_restofloop 2970
mict_totalloop 45663
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 120058
Contig coverage analysis ... Timing BFC loop total: 815607
bfc 1
Localtime: Mon Jun 15 17:09:04 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 17
Localtime: Mon Jun 15 17:09:04 2015
Unused reads: 1626501
bfc 8/0
0 Known 1: 2934
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 402
pft 13 / 119
[61] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 496
pft 15 / 116
[120] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 577
pft 15 / 114
[180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 832
pft 12 / 112
[240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1105
pft 10 / 118
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1241
pft 14 / 131
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1401
pft 17 / 125
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1606
pft 12 / 120
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1857
pft 13 / 145
[540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2123
pft 11 / 123
[600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2253
pft 12 / 122
[660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2319
pft 14 / 137
[720] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 2356
pft 15 / 137
[779] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2376
pft 17 / 132
[839] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 2386
pft 16 / 121
[898] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 2445
pft 15 / 112
[957] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2633
pft 16 / 109
[1017] +++++++++++++++++++++++++++++++++++++++++++++++++++++a++++a+ 2672
pft 13 / 115
[1075] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 2687
pft 14 / 118
[1134] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2939
pft 15 / 103
[1194] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3170
pft 12 / 135
[1254] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3290
pft 12 / 119
[1314] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3511
pft 11 / 123
[1374] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3679
pft 11 / 121
[1434] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3917
pft 11 / 124
[1494] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4000
pft 14 / 136
[1554] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++a+ 4021
pft 19 / 130
[1612] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 4067
pft 19 / 127
[1671] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4079
pft 20 / 110
[1731] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4116
pft 19 / 109
[1791] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 4149
pft 18 / 98
[1850] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4154
pft 19 / 84
[1910] ++dddd++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 4182
pft 19 / 132
[1965] ++++++++++++++++d+++++++++++a+++++++++++++++++++++++++++++++ 4510
pft 16 / 139
[2023] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4853
pft 11 / 117
[2083] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4905
pft 14 / 133
[2143] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 4957
pft 14 / 131
[2202] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 5163
pft 14 / 119
[2261] +++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 5252
pft 14 / 123
[2320] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5304
pft 14 / 118
[2380] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 5336
pft 16 / 109
[2439] +a++a++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 5785
pft 10 / 103
[2496] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5906
pft 13 / 117
[2556] +++++++++++++a++++++++++++++++++++++++++++++++++++++a+++++++ 6075
pft 12 / 113
[2614] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 6118
pft 12 / 108
[2673] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6368
pft 14 / 144
[2733] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6644
pft 11 / 119
[2793] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6900
pft 11 / 123
[2853] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7045
pft 13 / 134
[2913] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7098
pft 15 / 130
[2973] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7124
pft 20 / 132
[3033] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 7215
pft 17 / 124
[3092] +a+++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 7234
pft 20 / 113
[3150] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7328
pft 19 / 96
[3210] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7368
pft 18 / 91
[3270] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7414
pft 12 / 113
[3330] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 7420
pft 15 / 152
[3389] +++++++++++++++++++++++++++++d++++++++++++++++++++++++++++++ 7424
pft 20 / 170
[3448] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7793
pft 16 / 133
[3508] ++a+++++++++++++++++++++++++a+++++++++++++++++++++++++++++++ 7802
pft 25 / 155
[3566] ++++++++++++++++++++++++++++++++++++d++++++++a++++++++++++++ 7809
pft 24 / 151
[3624] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 7819
pft 26 / 129
[3682] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 7838
pft 24 / 142
[3741] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7842
pft 21 / 114
[3801] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 7847
pft 16 / 111
[3860] +++++a+++++++++++++++++++++++++++++++++++++a++++++++++++++++ 7929
pft 17 / 110
[3918] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7936
pft 12 / 155
[3978] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7947
pft 26 / 175
[4038] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 7958
pft 36 / 133
[4097] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7965
pft 15 / 149
[4157] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7972
pft 13 / 140
[4217] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7981
pft 20 / 147
[4277] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7990
pft 23 / 146
[4337] +++++++++++++a+++++a+++++++++a++++++++++++++++++++++a+++++++ 8003
pft 32 / 152
[4393] ++++++++++++++++++++++++a++++a++++++++++++++++a+++++++a+++++ 8007
pft 32 / 110
[4449] +++++++G++++++a+++++++++G+G+G++G+++++++G+++GG+++++++++++++++ 8009
pft 14 / 139
[4500] ++G++G+++++++++G+G++++++++G+G+++++G+GG++++GG+G+G+++GG+++G+GG 8013
pft 23 / 121
[4542] +G+G+G+G+G+GGGG++Ga++++GG+++++++G++++GGG+G+G++G+++G+G++++GG+ 8021
pft 36 / 104
[4578] ++G+GGGGGGGGG+++GG+GG+++++++++++G+++++++++G++++G+G++++++++++ 8025
pft 50 / 97
[4620] +++G++++a++++++++++++++++G+aaaaa++aaaaa+aaaadaddaaaaaa+++aaa 8031
pft 97 / 112
[4649] a+aaaaaaaaaaGGGGGaGGGGGGGGGGGGGGaaGGGGGGGGGGGGaaaGaGdGGGGGGG 8031
pft 45 / 97
[4650] GGGGGG+++aGGGGGpriv_ld addRead: 618813
priv_ld total: 695891
Timing BFC paf construct: 695965

ccon timings:
cct pre 3541
cct dir 6835
cct xcu 19971
cct tmp 2632
cct sw 380254
cct pic 2570
cct ico 165253
cct icm 0
cct upd 2863
cct del 0
cct rmz 2795
cct gcp 922

ccon i timings (4652):
ccit insglcc 293
ccit insglaro 1046
ccit insglact 122
ccit insgltot 4639
ccit pr 29707
ccit templ 4368
ccit index 2539
ccit biglccins 6547
ccit biglinterpol 905
ccit biglupdtags 521
ccit biglfpcri 532
ccit bigllgap 28222
ccit biglshiftread 4680
ccit bigltot 73050
ccit insgr 2615
ccit ucv 25542

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 4653
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:05 2015
Timing BFC analysereadcov: 21476
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 136
mict_fallout 9261
mict_newin 4381
mict_helper1 40910
mict_newin 4381
mict_restofloop 4436
mict_totalloop 76296
done.

-------------- Contig statistics ----------------
Contig id: 17
Contig length: 8031

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 4653 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 225 0 0
0 0 0
Avg. coverage 0.000 0.000 112.433 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 225
Avg. contig coverage: 112.433

Consensus contains: A: 1167 C: 2364 G: 2263 T: 1257 N: 0
IUPAC: 0 Funny: 0 *: 980
GC content: 65.622%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 77355
Localtime: Mon Jun 15 17:09:05 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 98136 cases.

P 1, marked 98136 reads.
Timing BFC edit tricky1: 59865
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 64697
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1536 cases.

Edited 1536 reads.
Localtime: Mon Jun 15 17:09:05 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:05 2015
Timing BFC edit tricky2: 42184

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 426 positions.
Localtime: Mon Jun 15 17:09:05 2015
Deleting superfluous gap columns (2) ... done, deleted 573 columns.
Localtime: Mon Jun 15 17:09:05 2015
Timing BFC edit single discrepancy, no HAF: 100356
bfc 12/0
Timing BFC delPSHP: 1080
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 29286
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 509
mict_pre 6
mict_shadow 141
mict_fallout 8425
mict_newin 4024
mict_helper1 35831
mict_newin 4024
mict_restofloop 4069
mict_totalloop 68396
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 187514
Contig coverage analysis ... Timing BFC loop total: 1283913
bfc 1
Localtime: Mon Jun 15 17:09:05 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 18
Localtime: Mon Jun 15 17:09:05 2015
Unused reads: 1621848
bfc 8/0
0 Known 1: 4653
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 444
pft 12 / 113
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 715
pft 9 / 117
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 999
pft 10 / 112
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1139
pft 11 / 116
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1188
pft 14 / 123
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1286
pft 15 / 129
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1313
pft 17 / 131
[421] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 1361
pft 19 / 129
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1580
pft 14 / 124
[540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1743
pft 8 / 119
[600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2004
pft 11 / 130
[660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2030
pft 15 / 134
[720] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2092
pft 19 / 116
[780] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2114
pft 19 / 94
[840] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2527
pft 12 / 118
[900] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2664
pft 11 / 132
[960] ++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 2678
pft 15 / 130
[1019] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 2688
pft 17 / 118
[1078] +++++++++++++++++a+++++++++++++++++++++++++++++++++++++a++++ 2749
pft 17 / 102
[1136] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2752
pft 17 / 83
[1196] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2756
pft 19 / 81
[1256] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3032
pft 16 / 90
[1316] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3183
pft 12 / 118
[1376] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3416
pft 13 / 136
[1436] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3575
pft 11 / 124
[1496] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3622
pft 18 / 132
[1556] +++++++++++++++++++++++++++++++++++++++++++++++a++++++++++++ 3633
pft 22 / 97
[1615] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3793
pft 22 / 90
[1674] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4081
pft 12 / 106
[1734] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4383
pft 9 / 118
[1794] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4642
pft 17 / 106
[1854] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4908
pft 9 / 118
[1914] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5051
pft 12 / 123
[1974] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5134
pft 16 / 120
[2034] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 5169
pft 18 / 97
[2093] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5461
pft 11 / 116
[2152] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5548
pft 12 / 148
[2212] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5633
pft 12 / 139
[2272] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5965
pft 11 / 122
[2332] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6092
pft 12 / 130
[2392] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6170
pft 13 / 139
[2452] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6199
pft 15 / 119
[2512] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 6328
pft 12 / 128
[2571] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6419
pft 13 / 124
[2631] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 6892
pft 11 / 126
[2690] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7039
pft 10 / 116
[2750] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 7251
pft 11 / 124
[2809] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7369
pft 13 / 124
[2869] ++++++++++++aa+++a++++aa+++++++++++++a+++++++++++a++a+++++++ 7414
pft 18 / 139
[2921] +++++aa++a+++++++++++++++++++++a+++++++a+++a++++++++++++++++ 7452
pft 15 / 132
[2975] ++++++++++++++++++++a+++++++++++++++++++++++++a+a+++++++++++ 7482
pft 16 / 114
[3032] +++++++++++++++++++a++++++++++++++++++a++++++++++++++a++++++ 7528
pft 14 / 108
[3089] ++++++a+++++++a+++++++++++++++++++++++++++++++++++++++++++++ 7631
pft 14 / 115
[3147] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 7636
pft 10 / 127
[3206] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 7790
pft 10 / 138
[3265] +++++++++a+++++++++++++a++++++++++++++++++++++++a+++++++++++ 7793
pft 14 / 141
[3322] ++++++++++++++++++++++++++++++++++++++++++a++++a++++++++++++ 7801
pft 16 / 148
[3380] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7809
pft 21 / 151
[3439] +++++++++++++++++++a+++a++++++++++++++++++++++++++++++++++++ 7818
pft 25 / 144
[3497] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 7828
pft 26 / 151
[3556] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7832
pft 25 / 115
[3616] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7836
pft 18 / 117
[3676] ++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++ 7842
pft 15 / 118
[3735] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8121
pft 11 / 114
[3795] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8337
pft 12 / 116
[3855] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8663
pft 11 / 99
[3915] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8683
pft 11 / 133
[3975] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8691
pft 11 / 136
[4035] ++++++++++++++++++++++++++++++++++++++++++a+a+++++++++++++++ 8695
pft 21 / 131
[4093] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8699
pft 14 / 162
[4153] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 8706
pft 41 / 144
[4212] ++a+++++++++++++++++++++++++++++++++++++++++++++++++d+++++++ 8711
pft 22 / 163
[4270] +++++++d++++++a++a++++++aa++a+++++++++++++a++++++++++++++++d 8721
pft 26 / 149
[4322] ++++dd++++++++++++++++++++++++a+++++++++++++++++++++++aaa+++ 8725
pft 27 / 96
[4376] +++++a++a++++++++++++aaaaaaaaaaaaaaaa+aaaaaaaaaaaa++aaaaaaaa 8726
pft 68 / 101
[4397] aaaaaaaa+a+aaaaaaaaaapriv_ld addRead: 565518
priv_ld total: 630093
Timing BFC paf construct: 630158

ccon timings:
cct pre 3266
cct dir 6734
cct xcu 18982
cct tmp 2461
cct sw 346225
cct pic 2453
cct ico 150660
cct icm 0
cct upd 2808
cct del 0
cct rmz 2703
cct gcp 538

ccon i timings (4398):
ccit insglcc 207
ccit insglaro 772
ccit insglact 101
ccit insgltot 3967
ccit pr 27663
ccit templ 4023
ccit index 2425
ccit biglccins 5091
ccit biglinterpol 897
ccit biglupdtags 537
ccit biglfpcri 529
ccit bigllgap 24573
ccit biglshiftread 4134
ccit bigltot 64739
ccit insgr 2631
ccit ucv 23870

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 4399
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:06 2015
Timing BFC analysereadcov: 20185
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 8
mict_shadow 140
mict_fallout 9329
mict_newin 4752
mict_helper1 37930
mict_newin 4752
mict_restofloop 4848
mict_totalloop 75515
done.

-------------- Contig statistics ----------------
Contig id: 18
Contig length: 8726

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 4399 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 189 0 0
0 0 0
Avg. coverage 0.000 0.000 96.690 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 189
Avg. contig coverage: 96.690

Consensus contains: A: 1418 C: 2477 G: 2584 T: 1286 N: 0
IUPAC: 0 Funny: 0 *: 961
GC content: 65.177%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 76705
Localtime: Mon Jun 15 17:09:06 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 88807 cases.

P 1, marked 88807 reads.
Timing BFC edit tricky1: 55435
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 59205
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1613 cases.

Edited 1613 reads.
Localtime: Mon Jun 15 17:09:06 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:06 2015
Timing BFC edit tricky2: 39470

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 380 positions.
Localtime: Mon Jun 15 17:09:06 2015
Deleting superfluous gap columns (2) ... done, deleted 600 columns.
Localtime: Mon Jun 15 17:09:06 2015
Timing BFC edit single discrepancy, no HAF: 94756
bfc 12/0
Timing BFC delPSHP: 1007
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 25927
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 544
mict_pre 6
mict_shadow 142
mict_fallout 8374
mict_newin 4378
mict_helper1 33963
mict_newin 4378
mict_restofloop 4370
mict_totalloop 68539
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 180306
Contig coverage analysis ... Timing BFC loop total: 1187262
bfc 1
Localtime: Mon Jun 15 17:09:06 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 2
bfc 5
bfc 6/0
bfc 7/0
Building new contig 19
Localtime: Mon Jun 15 17:09:06 2015
Unused reads: 1617449
bfc 8/0
0 Known 1: 4399
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 452
pft 14 / 136
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 576
pft 13 / 124
[121] ++++++++++++++++a+++++++++++++++++++++++++a+++++++++++++++++ 645
pft 13 / 118
[179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 930
pft 13 / 124
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1129
pft 11 / 114
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1338
pft 11 / 124
[359] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1402
pft 11 / 130
[419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1585
pft 13 / 135
[479] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 1800
pft 9 / 128
[538] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 1921
pft 12 / 137
[597] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1942
pft 17 / 141
[657] +a+++a+++++a++++++++++++++++++++++++++++++++++++++++++++++++ 1950
pft 19 / 119
[714] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1959
pft 25 / 118
[774] ++++++++++++++++++++++++++++++++++++++++++a++++a++++++++++++ 1963
pft 20 / 89
[832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2106
pft 19 / 97
[892] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2661
pft 9 / 113
[952] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2808
pft 13 / 121
[1012] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2836
pft 15 / 118
[1072] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2844
pft 15 / 107
[1132] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 2853
pft 13 / 124
[1191] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 3131
pft 12 / 113
[1250] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 3298
pft 12 / 129
[1309] ++++++++++++++++++++a+++++++++++++++a+++a+++++++++++a+++++++ 3330
pft 15 / 123
[1365] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3449
pft 15 / 107
[1424] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3757
pft 14 / 122
[1484] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3831
pft 14 / 141
[1544] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 3892
pft 11 / 129
[1603] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4055
pft 10 / 130
[1663] ++++++++++++++a+++++++++++a+++++++++++++++++++++++++++++++++ 4309
pft 11 / 138
[1721] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4320
pft 10 / 143
[1781] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 4323
pft 11 / 146
[1840] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 4326
pft 17 / 152
[1899] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4339
pft 18 / 160
[1959] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4442
pft 15 / 136
[2019] ++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++ 4456
pft 20 / 143
[2078] ++++++a++++++++a++++++++++++++++++++++++a+++++++++++++++++++ 4611
pft 17 / 151
[2135] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4748
pft 10 / 130
[2195] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 4757
pft 22 / 146
[2254] ++a++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 4766
pft 17 / 139
[2312] +++++++++++++++++++++++++++++++a+++++++++++++a++++++++++++++ 4775
pft 19 / 127
[2370] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4786
pft 19 / 122
[2430] +++++++++++++++++++++++++++++++++++++++++++++++++++++a+++a++ 4795
pft 21 / 119
[2488] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 4901
pft 17 / 135
[2547] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4924
pft 11 / 135
[2607] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4940
pft 25 / 136
[2667] +++++++++++++++++++++++++a++++++++++++++++++++++++++++++++++ 5161
pft 12 / 133
[2726] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5200
pft 10 / 136
[2786] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 5218
pft 13 / 153
[2845] ++++++++++++G+++++++++++++++++GG+G++++++++++++++++++++++++++ 5223
pft 17 / 147
[2901] +++++++++++++++++++++G++++a+G+++++++++++++++++++++G+++++++G+ 5225
pft 16 / 152
[2956] +G+G++G+G++++G++++GG++++++G+++++++++++++++++++++++++G+++++++ 5236
pft 17 / 157
[3007] ++++++++++++++++++++++++++++G++++G++++++++++++++++++++++++++ 5242
pft 30 / 141
[3065] +++++++++++a++++++G++++G++++++++++++++++++++++++++++++++++++ 5253
pft 31 / 112
[3122] ++++++++G+GG+GG+++G+G+++++GGGG++GGGGGGG++GGGaG+G+++GG+G+G+GG 5261
pft 25 / 114
[3151] GGGGGGGGGGGGGGGGGGGGGGGGG+G++G++G++G++G+G+GG++GGGG++G+++G++G 5262
pft 28 / 73
[3172] +G+++++G++++G++++++++++++++++++aaaaaaaaaaaaaaaaaaaaaGaaaGGGa 5267
pft 93 / 103
[3199] GGGGGGGGGGGGGGGGGGGGaaaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5267
pft 34 / 94
[3199] GGGGGGGGGGGGGpriv_ld addRead: 447088
priv_ld total: 499071
Timing BFC paf construct: 499137

ccon timings:
cct pre 2503
cct dir 5111
cct xcu 16913
cct tmp 1794
cct sw 278300
cct pic 1741
cct ico 114002
cct icm 0
cct upd 2068
cct del 0
cct rmz 1937
cct gcp 717

ccon i timings (3198):
ccit insglcc 121
ccit insglaro 439
ccit insglact 52
ccit insgltot 2702
ccit pr 20045
ccit templ 2881
ccit index 1745
ccit biglccins 3703
ccit biglinterpol 629
ccit biglupdtags 385
ccit biglfpcri 367
ccit bigllgap 19939
ccit biglshiftread 3040
ccit bigltot 51042
ccit insgr 1817
ccit ucv 18106

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3199
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:07 2015
Timing BFC analysereadcov: 16246
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 9
mict_shadow 118
mict_fallout 6189
mict_newin 2793
mict_helper1 27342
mict_newin 2793
mict_restofloop 2908
mict_totalloop 50391
done.

-------------- Contig statistics ----------------
Contig id: 19
Contig length: 5267

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3199 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 204 0 0
0 0 0
Avg. coverage 0.000 0.000 121.120 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 204
Avg. contig coverage: 121.120

Consensus contains: A: 913 C: 1531 G: 1364 T: 782 N: 0
IUPAC: 0 Funny: 0 *: 677
GC content: 63.072%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 51069
Localtime: Mon Jun 15 17:09:07 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 71511 cases.

P 1, marked 71511 reads.
Timing BFC edit tricky1: 44398
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 46034
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1102 cases.

Edited 1102 reads.
Localtime: Mon Jun 15 17:09:07 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:07 2015
Timing BFC edit tricky2: 29434

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 306 positions.
Localtime: Mon Jun 15 17:09:07 2015
Deleting superfluous gap columns (2) ... done, deleted 386 columns.
Localtime: Mon Jun 15 17:09:07 2015
Timing BFC edit single discrepancy, no HAF: 68065
bfc 12/0
Timing BFC delPSHP: 736
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 19787
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 340
mict_pre 6
mict_shadow 103
mict_fallout 5934
mict_newin 2730
mict_helper1 26124
mict_newin 2730
mict_restofloop 2690
mict_totalloop 48026
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 134276
Timing BFC loop total: 912344
bfc 1
Localtime: Mon Jun 15 17:09:07 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 20
Localtime: Mon Jun 15 17:09:07 2015
Unused reads: 1614250
bfc 8/0
0 Known 1: 3199
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 486
pft 11 / 118
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 691
pft 11 / 118
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 829
pft 13 / 129
[181] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 1109
pft 11 / 114
[240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1327
pft 11 / 122
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1520
pft 11 / 121
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1603
pft 13 / 133
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1645
pft 17 / 129
[480] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 1659
pft 15 / 120
[539] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1721
pft 16 / 107
[599] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 1847
pft 15 / 104
[658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2134
pft 15 / 120
[718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2201
pft 12 / 132
[778] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2270
pft 14 / 135
[838] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 2460
pft 12 / 127
[897] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2657
pft 10 / 125
[957] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2845
pft 12 / 119
[1017] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2916
pft 15 / 133
[1077] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2928
pft 18 / 127
[1137] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3021
pft 21 / 103
[1197] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++a+++ 3031
pft 20 / 99
[1255] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 3039
pft 22 / 101
[1314] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 3045
pft 22 / 78
[1373] +++++++++a+++a++++++++++++++++++a+++++++++++++++++++++++++++ 3098
pft 18 / 87
[1430] +++a++++++++++++++++++++++++a+++++++++++++++++++++++++++++++ 3134
pft 19 / 145
[1488] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3142
pft 26 / 132
[1548] ++++++aaa++++++++aaaaaaaapriv_ld addRead: 190893
priv_ld total: 212593
Timing BFC paf construct: 212658

ccon timings:
cct pre 1173
cct dir 1431
cct xcu 5213
cct tmp 884
cct sw 117835
cct pic 850
cct ico 51418
cct icm 0
cct upd 964
cct del 0
cct rmz 961
cct gcp 87

ccon i timings (1560):
ccit insglcc 113
ccit insglaro 400
ccit insglact 57
ccit insgltot 1641
ccit pr 9636
ccit templ 1224
ccit index 829
ccit biglccins 1545
ccit biglinterpol 326
ccit biglupdtags 200
ccit biglfpcri 194
ccit bigllgap 7883
ccit biglshiftread 1605
ccit bigltot 21179
ccit insgr 899
ccit ucv 8377

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1561
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:08 2015
Timing BFC analysereadcov: 7038
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 46
mict_fallout 3244
mict_newin 1665
mict_helper1 12791
mict_newin 1665
mict_restofloop 1710
mict_totalloop 26142
done.

-------------- Contig statistics ----------------
Contig id: 20
Contig length: 3142

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1561 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 159 0 0
0 0 0
Avg. coverage 0.000 0.000 94.207 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 159
Avg. contig coverage: 94.207

Consensus contains: A: 534 C: 931 G: 907 T: 420 N: 0
IUPAC: 0 Funny: 0 *: 350
GC content: 65.831%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 26461
Localtime: Mon Jun 15 17:09:08 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 30220 cases.

P 1, marked 30220 reads.
Timing BFC edit tricky1: 17822
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 17492
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 570 cases.

Edited 570 reads.
Localtime: Mon Jun 15 17:09:08 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:08 2015
Timing BFC edit tricky2: 13628

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 116 positions.
Localtime: Mon Jun 15 17:09:08 2015
Deleting superfluous gap columns (2) ... done, deleted 224 columns.
Localtime: Mon Jun 15 17:09:08 2015
Timing BFC edit single discrepancy, no HAF: 30920
bfc 12/0
Timing BFC delPSHP: 195
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 7658
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 180
mict_pre 7
mict_shadow 46
mict_fallout 2963
mict_newin 1575
mict_helper1 11609
mict_newin 1575
mict_restofloop 1617
mict_totalloop 24011
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 58434
Timing BFC loop total: 393277
bfc 1
Localtime: Mon Jun 15 17:09:08 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 21
Localtime: Mon Jun 15 17:09:08 2015
Unused reads: 1612689
bfc 8/0
0 Known 1: 1561
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 608
pft 13 / 131
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 751
pft 11 / 121
[121] ++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 1002
pft 10 / 120
[180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1192
pft 10 / 118
[240] ++++++++++++++++++++++++++++++++++++++++++++++++a+++a+++++++ 1257
pft 12 / 132
[298] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 1273
pft 14 / 132
[357] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1532
pft 13 / 119
[417] +++++++++++++++++++++++++a+++++++++++++++++++++++++++a++++++ 1595
pft 14 / 124
[475] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 1638
pft 15 / 112
[534] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1709
pft 17 / 90
[593] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1716
pft 15 / 90
[653] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1742
pft 17 / 79
[713] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2003
pft 12 / 102
[773] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2320
pft 13 / 126
[833] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2561
pft 14 / 116
[893] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2675
pft 14 / 118
[953] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2744
pft 15 / 111
[1013] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2750
pft 17 / 101
[1073] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3036
pft 14 / 101
[1133] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3255
pft 10 / 118
[1193] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3388
pft 11 / 121
[1253] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3550
pft 12 / 127
[1313] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 3626
pft 18 / 131
[1372] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 3667
pft 14 / 119
[1431] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3675
pft 15 / 106
[1491] +++++++++++++++++++++++++++++a+++++++++++++++++a++++++++++++ 3721
pft 15 / 121
[1549] ++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 3997
pft 19 / 156
[1608] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4213
pft 11 / 123
[1668] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4311
pft 12 / 128
[1728] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4387
pft 18 / 135
[1788] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4449
pft 15 / 115
[1848] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4743
pft 14 / 121
[1908] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 4809
pft 14 / 122
[1967] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5030
pft 12 / 122
[2027] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5044
pft 12 / 132
[2087] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5050
pft 13 / 123
[2147] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5069
pft 14 / 142
[2206] a++a++++aa+a+++++++a++++a+++++++++++++++++++++++a+++++++++++ 5321
pft 10 / 140
[2259] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5628
pft 15 / 135
[2319] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5698
pft 13 / 130
[2379] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5853
pft 14 / 124
[2439] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6312
pft 12 / 113
[2499] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 6329
pft 14 / 118
[2558] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6342
pft 15 / 111
[2618] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6379
pft 10 / 140
[2678] +++++++++++++++++a++++++++++++++++++a++++++++++++a++++++++++ 6381
pft 12 / 154
[2734] a+++++++++aa+++aa+a++++++a+++aa++a++++++a+++a++++a+++++a+a++ 6386
pft 20 / 157
[2780] +++++++++++a++++++++++a+aa++++aa+++++++++++++++++++a++++a+++ 6393
pft 24 / 155
[2832] +++++++a++++++++a+++++++++a++++++a++++++++a++++++++a++++++++ 6400
pft 29 / 130
[2886] ++a++++++++++++++++++++++++++++++++++++++++++++++aa+a++++++a 6410
pft 29 / 145
[2941] ++a++++a++++++++++++++a+++++++++++++++++a+++++++++++++++++++ 6419
pft 21 / 121
[2997] +++++++++++++a+++++++++++a+++++++++++++++++++++a++++++++++++ 6425
pft 20 / 104
[3054] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6432
pft 17 / 161
[3114] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6441
pft 29 / 160
[3174] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6448
pft 32 / 126
[3234] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6457
pft 27 / 166
[3294] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6460
pft 27 / 113
[3354] +++++++a+++++++++++++++++++++++++++a+++++++++++++++++++a++++ 6462
pft 16 / 169
[3411] +++++++++++++a++++++++a+++++++++++++++++++a+++++++++++++++++ 6465
pft 47 / 108
[3468] ++++aaaa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaaaaaaaaapriv_ld addRead:
459597
priv_ld total: 513536
Timing BFC paf construct: 513585

ccon timings:
cct pre 2649
cct dir 4614
cct xcu 15944
cct tmp 1947
cct sw 283162
cct pic 1895
cct ico 121566
cct icm 0
cct upd 2186
cct del 0
cct rmz 2073
cct gcp 526

ccon i timings (3472):
ccit insglcc 204
ccit insglaro 689
ccit insglact 95
ccit insgltot 3353
ccit pr 21999
ccit templ 3132
ccit index 1932
ccit biglccins 4414
ccit biglinterpol 730
ccit biglupdtags 423
ccit biglfpcri 376
ccit bigllgap 19048
ccit biglshiftread 3685
ccit bigltot 53334
ccit insgr 2064
ccit ucv 18982

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3473
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:08 2015
Timing BFC analysereadcov: 15978
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 115
mict_fallout 6877
mict_newin 3463
mict_helper1 28742
mict_newin 3463
mict_restofloop 3471
mict_totalloop 56424
done.

-------------- Contig statistics ----------------
Contig id: 21
Contig length: 6466

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3473 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 228 0 0
0 0 0
Avg. coverage 0.000 0.000 102.822 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 228
Avg. contig coverage: 102.822

Consensus contains: A: 1053 C: 1862 G: 1856 T: 922 N: 0
IUPAC: 0 Funny: 0 *: 773
GC content: 65.308%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 57122
Localtime: Mon Jun 15 17:09:08 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 72694 cases.

P 1, marked 72694 reads.
Timing BFC edit tricky1: 45092
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 47182
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 389 positions.
Localtime: Mon Jun 15 17:09:08 2015
Deleting superfluous gap columns (2) ... done, deleted 98 columns.
Localtime: Mon Jun 15 17:09:08 2015
Timing BFC edit single discrepancy, no HAF: 49341
bfc 12/0
Timing BFC delPSHP: 667
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: 262
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 285
mict_pre 8
mict_shadow 103
mict_fallout 6769
mict_newin 3467
mict_helper1 28187
mict_newin 3467
mict_restofloop 3494
mict_totalloop 55463
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 155242
Contig coverage analysis ... Timing BFC loop total: 887238
bfc 1
Localtime: Mon Jun 15 17:09:09 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 22
Localtime: Mon Jun 15 17:09:09 2015
Unused reads: 1609216
bfc 8/0
0 Known 1: 3473
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 491
pft 11 / 130
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 664
pft 14 / 125
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 697
pft 20 / 150
[181] ++++++++++++++++++++++++++a++++++++++a++++++++++++++++++++++ 808
pft 16 / 124
[239] +++++++++++++++++++a+++++a++++a+a+++++++a++a+++++++++a++++++ 860
pft 15 / 119
[292] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1121
pft 12 / 117
[352] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 1130
pft 13 / 126
[411] ++++++++++++++++++++++++++++++++++++++++++++a+++++++a+++++++ 1436
pft 11 / 120
[469] ++aaa+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1656
pft 11 / 116
[526] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1743
pft 14 / 116
[586] +++++++a++++++++++a++++a+++a++++++++++++aa++++++++++++++++++ 1747
pft 18 / 102
[640] +++++++++++++++++a++++++a+++++++++++++++++++++++++++++++++++ 1751
pft 14 / 94
[698] +++++++++++++++++++++a++++++++++++++++a++aa+++a++++a+++a++++ 1759
pft 14 / 100
[751] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 2135
pft 13 / 99
[810] ++++++++++aa++++++++++++++++++++++++++++++++++++++++++++++++ 2140
pft 15 / 129
[868] ++++++++a++++++++a+++++++++++++++++++++++++++aaaaaaaaaaaaaaa 2146
pft 43 / 123
[910] aaaaaaaaaaaaapriv_ld addRead: 117013
priv_ld total: 131156
Timing BFC paf construct: 131222

ccon timings:
cct pre 703
cct dir 838
cct xcu 3727
cct tmp 531
cct sw 73680
cct pic 506
cct ico 29615
cct icm 0
cct upd 572
cct del 0
cct rmz 559
cct gcp 191

ccon i timings (909):
ccit insglcc 99
ccit insglaro 361
ccit insglact 53
ccit insgltot 1191
ccit pr 5559
ccit templ 695
ccit index 488
ccit biglccins 634
ccit biglinterpol 183
ccit biglupdtags 107
ccit biglfpcri 105
ccit bigllgap 4093
ccit biglshiftread 926
ccit bigltot 11715
ccit insgr 511
ccit ucv 4942

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 910
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:09 2015
Timing BFC analysereadcov: 4106
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 8
mict_shadow 28
mict_fallout 2042
mict_newin 1203
mict_helper1 7519
mict_newin 1203
mict_restofloop 1176
mict_totalloop 16402
done.

-------------- Contig statistics ----------------
Contig id: 22
Contig length: 2146

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 910 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 154 0 0
0 0 0
Avg. coverage 0.000 0.000 80.045 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 154
Avg. contig coverage: 80.045

Consensus contains: A: 315 C: 644 G: 614 T: 378 N: 0
IUPAC: 0 Funny: 0 *: 195
GC content: 64.480%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 16628
Localtime: Mon Jun 15 17:09:09 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 16353 cases.

P 1, marked 16353 reads.
Timing BFC edit tricky1: 10159
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 11279
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 333 cases.

Edited 333 reads.
Localtime: Mon Jun 15 17:09:09 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:09 2015
Timing BFC edit tricky2: 8520

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 83 positions.
Localtime: Mon Jun 15 17:09:09 2015
Deleting superfluous gap columns (2) ... done, deleted 119 columns.
Localtime: Mon Jun 15 17:09:09 2015
Timing BFC edit single discrepancy, no HAF: 16628
bfc 12/0
Timing BFC delPSHP: 109
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 4366
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 86
mict_pre 5
mict_shadow 28
mict_fallout 1914
mict_newin 1097
mict_helper1 6857
mict_newin 1097
mict_restofloop 1077
mict_totalloop 15279
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 38389
Timing BFC loop total: 242083
bfc 1
Localtime: Mon Jun 15 17:09:09 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 23
Localtime: Mon Jun 15 17:09:09 2015
Unused reads: 1608306
bfc 8/0
0 Known 1: 910
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 586
pft 10 / 111
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 847
pft 10 / 116
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1131
pft 11 / 119
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1177
pft 14 / 127
[240] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1224
pft 15 / 118
[300] +++++++++a++++++++++++++++++++++++a+++++++++++++++++++++++++ 1353
pft 14 / 122
[358] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1583
pft 11 / 117
[418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1802
pft 12 / 127
[478] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2055
pft 12 / 112
[538] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2217
pft 17 / 116
[598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2264
pft 20 / 141
[658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2323
pft 20 / 114
[718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2506
pft 13 / 116
[778] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2567
pft 14 / 133
[838] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 2585
pft 16 / 115
[897] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 2618
pft 18 / 111
[956] ++++++++++++++++++++++++++++++++++++++++++a+++++++++a+++++++ 2639
pft 20 / 96
[1014] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2770
pft 14 / 99
[1074] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2796
pft 15 / 99
[1134] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2803
pft 20 / 82
[1194] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3089
pft 16 / 95
[1254] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3226
pft 12 / 121
[1314] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3516
pft 10 / 120
[1374] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3666
pft 16 / 146
[1434] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3707
pft 17 / 119
[1494] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3757
pft 19 / 92
[1554] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3803
pft 20 / 81
[1614] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4192
pft 15 / 110
[1674] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4265
pft 12 / 124
[1734] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 4306
pft 12 / 120
[1793] ++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 4497
pft 16 / 141
[1852] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4726
pft 11 / 126
[1912] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4867
pft 11 / 131
[1972] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4924
pft 13 / 141
[2032] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5134
pft 12 / 128
[2092] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5215
pft 16 / 158
[2152] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5271
pft 15 / 128
[2212] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 5283
pft 13 / 126
[2271] +++++++++++a++++++++++++++++++++++++++++++++++++++++++++++++ 5331
pft 15 / 118
[2330] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 5423
pft 13 / 142
[2389] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5432
pft 11 / 141
[2449] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 5589
pft 12 / 140
[2508] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5598
pft 22 / 169
[2568] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5609
pft 29 / 154
[2628] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5621
pft 29 / 144
[2688] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5703
pft 24 / 133
[2748] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5711
pft 24 / 136
[2808] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5721
pft 22 / 115
[2868] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5726
pft 28 / 103
[2928] ++++++++++++++++++++++++++++++++++a+++++++++++++a+++++++++++ 5731
pft 29 / 107
[2986] ++++++++++++++a++++++++++a+++++++GGGGG++G++G+++++++++++++++G 5738
pft 25 / 136
[3036] ++G+++++++++++++++++++++++++++G+G+++++++++++++G++GG+GG++++++ 5746
pft 13 / 133
[3088] ++++++GGG++++++++++GG+++++++++++++++++++++G+++++++++G++++++G 5754
pft 16 / 141
[3140] +++++G++G+++G++GGG++++GGG++++++G++++++++++++++++G++G+GGG+G+a 5764
pft 21 / 122
[3183] ++G+++G+++++++++G+GGGGG+GGG+++GGG+G+++a+++++++++++++++++++++ 5767
pft 17 / 110
[3227] +++++++++++G++++++G+++++++G++++++++++G+++G+GG++++++++++G++G+ 5771
pft 15 / 145
[3278] ++++++G+GGGG+GGGGG+G++G++G+++++GGGG+GGGGGGG+++++G++G+GG+GGGG 5772
pft 16 / 109
[3306] ++G+GG++++++G+G+GG++G++aGGG+GGGGGGGGG+++G+GGG+G+GG+GGG+G+GG+ 5781
pft 24 / 107
[3331] GGGG++GG++GGG++G++GGGGG++G+++GGGGG++GGG+GGGG+GGGGGG+GG+GGGG+ 5796
pft 19 / 72
[3351] GGG++GG+G+G+++GG+GGGGGGGGGGGGGGGGGGG++GGGGGGGG++++++GGG+++G+ 5797
pft 21 / 67
[3371] G++G++aaaaaaaa++G++GG++GGG++GG+++++GG+G++++GGG+GG++G+GGG+GGG 5801
pft 83 / 126
[3398] G+GG+GGGGGG+GG+G+GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5801
pft 9 / 92
[3403] GGGGGGGGG+GGGGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGaGGGGGG 5801
pft 56 / 82
[3404] GGGGGGGGGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld
addRead: 467322
priv_ld total: 529522
Timing BFC paf construct: 529572

ccon timings:
cct pre 2777
cct dir 4167
cct xcu 16621
cct tmp 2090
cct sw 291031
cct pic 1846
cct ico 119255
cct icm 0
cct upd 2114
cct del 0
cct rmz 2053
cct gcp 1188

ccon i timings (3403):
ccit insglcc 192
ccit insglaro 602
ccit insglact 76
ccit insgltot 3088
ccit pr 21733
ccit templ 3100
ccit index 1921
ccit biglccins 3576
ccit biglinterpol 715
ccit biglupdtags 424
ccit biglfpcri 397
ccit bigllgap 20248
ccit biglshiftread 3753
ccit bigltot 52674
ccit insgr 1943
ccit ucv 18391

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3404
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:09 2015
Timing BFC analysereadcov: 15515
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 6
mict_shadow 107
mict_fallout 6650
mict_newin 3192
mict_helper1 28404
mict_newin 3192
mict_restofloop 3252
mict_totalloop 53997
done.

-------------- Contig statistics ----------------
Contig id: 23
Contig length: 5801

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3404 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 207 0 0
0 0 0
Avg. coverage 0.000 0.000 111.155 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 207
Avg. contig coverage: 111.155

Consensus contains: A: 936 C: 1593 G: 1671 T: 850 N: 0
IUPAC: 0 Funny: 0 *: 751
GC content: 64.634%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 54776
Localtime: Mon Jun 15 17:09:09 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 72747 cases.

P 1, marked 72747 reads.
Timing BFC edit tricky1: 42562
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 44400
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 343 positions.
Localtime: Mon Jun 15 17:09:10 2015
Deleting superfluous gap columns (2) ... done, deleted 94 columns.
Localtime: Mon Jun 15 17:09:10 2015
Timing BFC edit single discrepancy, no HAF: 46200
bfc 12/0
Timing BFC delPSHP: 666
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: 241
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 238
mict_pre 7
mict_shadow 104
mict_fallout 6513
mict_newin 3100
mict_helper1 27843
mict_newin 3100
mict_restofloop 3091
mict_totalloop 53001
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 148310
Contig coverage analysis ... Timing BFC loop total: 885148
bfc 1
Localtime: Mon Jun 15 17:09:10 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 24
Localtime: Mon Jun 15 17:09:10 2015
Unused reads: 1604902
bfc 8/0
0 Known 1: 3404
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 432
pft 12 / 119
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 564
pft 11 / 125
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 843
pft 11 / 122
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 979
pft 12 / 126
[241] +++++++++++++++++++++++++++++++++++++++++++++++++++++a++++++ 1051
pft 17 / 129
[300] ++++++++++++++++++++++++a++++++++++a++++++++++++++++++++++++ 1088
pft 18 / 114
[358] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 1233
pft 19 / 101
[417] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1439
pft 10 / 122
[477] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1487
pft 17 / 126
[537] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1541
pft 20 / 93
[597] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1543
pft 19 / 77
[657] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1933
pft 13 / 105
[717] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2164
pft 12 / 130
[777] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2585
pft 10 / 120
[837] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2800
pft 11 / 117
[897] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2830
pft 14 / 130
[957] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2867
pft 14 / 128
[1017] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2880
pft 22 / 113
[1077] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2885
pft 20 / 94
[1137] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 2891
pft 18 / 101
[1196] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3016
pft 16 / 93
[1256] ++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++ 3462
pft 13 / 97
[1315] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3777
pft 10 / 121
[1375] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3797
pft 18 / 97
[1434] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4189
pft 15 / 89
[1494] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4574
pft 13 / 105
[1554] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4769
pft 12 / 137
[1614] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4807
pft 12 / 135
[1674] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4910
pft 13 / 132
[1734] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5054
pft 14 / 129
[1794] ++++a++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 5091
pft 16 / 113
[1852] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5123
pft 18 / 101
[1912] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5375
pft 14 / 102
[1972] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 5452
pft 12 / 119
[2031] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5809
pft 13 / 104
[2090] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5859
pft 14 / 114
[2150] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 5876
pft 21 / 100
[2209] ++++++++a+++++++++++++++++++++++++++a+++++aaaa++++++++++++++ 5881
pft 10 / 143
[2263] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5886
pft 28 / 171
[2323] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5893
pft 34 / 118
[2382] ++++++++++++++++aaaaaaaaaaaaaaaaaapriv_ld addRead: 284981
priv_ld total: 318272
Timing BFC paf construct: 318337

ccon timings:
cct pre 1738
cct dir 2915
cct xcu 7932
cct tmp 1272
cct sw 172920
cct pic 1319
cct ico 78070
cct icm 0
cct upd 1475
cct del 0
cct rmz 1400
cct gcp 134

ccon i timings (2396):
ccit insglcc 222
ccit insglaro 724
ccit insglact 90
ccit insgltot 2773
ccit pr 14826
ccit templ 2017
ccit index 1288
ccit biglccins 2516
ccit biglinterpol 524
ccit biglupdtags 314
ccit biglfpcri 293
ccit bigllgap 11219
ccit biglshiftread 2598
ccit bigltot 31673
ccit insgr 1382
ccit ucv 12428

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2397
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:10 2015
Timing BFC analysereadcov: 10558
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 78
mict_fallout 5362
mict_newin 3172
mict_helper1 19692
mict_newin 3172
mict_restofloop 3238
mict_totalloop 43881
done.

-------------- Contig statistics ----------------
Contig id: 24
Contig length: 5893

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2397 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 168 0 0
0 0 0
Avg. coverage 0.000 0.000 73.945 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 168
Avg. contig coverage: 73.945

Consensus contains: A: 929 C: 1913 G: 1668 T: 804 N: 0
IUPAC: 0 Funny: 0 *: 579
GC content: 67.388%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 44414
Localtime: Mon Jun 15 17:09:10 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 41233 cases.

P 1, marked 41233 reads.
Timing BFC edit tricky1: 28622
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 29931
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 907 cases.

Edited 907 reads.
Localtime: Mon Jun 15 17:09:10 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:10 2015
Timing BFC edit tricky2: 20758

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 227 positions.
Localtime: Mon Jun 15 17:09:10 2015
Deleting superfluous gap columns (2) ... done, deleted 372 columns.
Localtime: Mon Jun 15 17:09:10 2015
Timing BFC edit single discrepancy, no HAF: 46082
bfc 12/0
Timing BFC delPSHP: 589
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 13263
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 380
mict_pre 6
mict_shadow 74
mict_fallout 4988
mict_newin 2925
mict_helper1 18227
mict_newin 2925
mict_restofloop 3031
mict_totalloop 41009
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 97377
Contig coverage analysis ... Timing BFC loop total: 611594
bfc 1
Localtime: Mon Jun 15 17:09:10 2015

bfc 2
Timing BFC prelim1: 1
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 25
Localtime: Mon Jun 15 17:09:10 2015
Unused reads: 1602505
bfc 8/0
0 Known 1: 2397
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 451
pft 12 / 117
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 634
pft 12 / 124
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 853
pft 13 / 118
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1017
pft 13 / 115
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1232
pft 12 / 116
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1478
pft 14 / 129
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1694
pft 12 / 129
[421] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 1721
pft 19 / 128
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1739
pft 18 / 119
[540] +++++++++++++++++a+++++++++++++++++++++++++++++++++a++++++++ 1795
pft 18 / 114
[598] ++++aa++++++++++++++++++a++++++++++++++++++++a++++++++++++++ 1839
pft 20 / 113
[653] a++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 1935
pft 19 / 115
[712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2278
pft 11 / 119
[772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2392
pft 15 / 129
[832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2688
pft 11 / 121
[892] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2766
pft 18 / 129
[952] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 2847
pft 19 / 124
[1011] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2889
pft 16 / 119
[1071] ++a++++++++++++++++++++++++++++++++++a+++a++++++++++++++++++ 2941
pft 19 / 105
[1128] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2952
pft 20 / 103
[1188] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 2961
pft 18 / 88
[1247] ++++++++a+++++++++++++++++++++++++a+++++++++++++++++++++a+++ 2994
pft 18 / 91
[1304] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 3030
pft 18 / 86
[1363] ++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++ 3048
pft 15 / 92
[1422] +++a++a++++++++a++++++++++++++++++++++++++++++++++++++++++++ 3338
pft 16 / 128
[1479] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3408
pft 14 / 135
[1539] +++++++++++++++++++++a++a+++++++++++++++++++++++++++++++++++ 3470
pft 14 / 113
[1597] +++++++++++++++++++++++++++++++a++++++++++++a+++++++++++++++ 3614
pft 14 / 114
[1655] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3855
pft 14 / 130
[1715] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4162
pft 10 / 122
[1775] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4279
pft 10 / 126
[1835] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4342
pft 12 / 125
[1895] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4367
pft 13 / 123
[1955] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 4386
pft 13 / 115
[2014] ++++++++++++++++++++++a+++++aa++++++++++++++++++++++++++++++ 4809
pft 12 / 126
[2071] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4982
pft 11 / 119
[2131] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4998
pft 16 / 133
[2191] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5246
pft 11 / 119
[2251] +++++++++++++++++++++++++++++++++++++++++++++++a++++++++a+++ 5403
pft 13 / 114
[2309] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 5488
pft 12 / 119
[2368] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 5570
pft 9 / 137
[2427] +++++a+++a+++aa+++++++++++++++++++++++++++++++++a+++++++++++ 5572
pft 18 / 141
[2482] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++a+a+ 5586
pft 22 / 152
[2539] ++++++++a+++++++++++++++++++++++++a+++++++++a+++++++++++++++ 5598
pft 21 / 140
[2596] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5602
pft 21 / 112
[2656] ++++++++++++++++++++++++++++++++++++++++++a+++++++GGG+G+G+++ 5643
pft 14 / 111
[2710] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5649
pft 10 / 137
[2770] +++G++++G++G+++++++++G++++++++++++++++++++++++++++++++++++++ 5656
pft 17 / 147
[2826] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5856
pft 15 / 137
[2886] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5924
pft 12 / 128
[2946] ++++++a++++++++++++++++++aa++aa+++++++++++++++++++++++++++++ 6177
pft 11 / 124
[3001] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 6432
pft 12 / 122
[3060] +++++++++++++++++++d+++++a+++++++++++++++++++a+a++++++++++++ 6508
pft 12 / 130
[3116] +++++++++++++d+++++++++++++++++++++a++++++++++a+++++++++++++ 6563
pft 11 / 127
[3173] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6845
pft 11 / 116
[3233] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6908
pft 14 / 128
[3293] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 6919
pft 12 / 130
[3352] ++++++d+++++++++++++++++++a+++++++++++++++++++++++++++++++++ 6951
pft 12 / 142
[3410] +++++++++++++++++++++++++++++++++d++++++++++++++++++d+++++++ 6959
pft 12 / 147
[3468] ++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++ 6976
pft 12 / 159
[3527] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7466
pft 12 / 113
[3587] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7631
pft 13 / 118
[3647] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+a 7686
pft 14 / 134
[3705] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7747
pft 15 / 130
[3765] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7802
pft 15 / 114
[3825] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7823
pft 13 / 100
[3885] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7961
pft 12 / 142
[3945] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7967
pft 14 / 149
[4005] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7975
pft 19 / 157
[4065] +++++++++a+++++a++++++++++++++++++++++++++++++++++++++++++++ 7985
pft 22 / 141
[4123] +++a+++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 7992
pft 25 / 139
[4181] ++++++++++++++++a+++++++++++++++++++++++++++++++++a+++++++++ 7996
pft 32 / 105
[4239] +++++++++aa++++++++++++++++++++++++++a++++++++++++++++++++++ 8010
pft 21 / 150
[4296] +++++a++++a++++++++++++++++++++++++++++++a+++++++++++++a++++ 8020
pft 38 / 147
[4352] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8026
pft 29 / 132
[4412] +++++++++++++++++++++++++++++++G+G++++++++G+++++++++G+++++G+ 8029
pft 17 / 164
[4467] +++++++++GG+++++++++++++++++++++++++++++++++++++++++++++++++ 8367
pft 14 / 117
[4525] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8376
pft 11 / 125
[4585] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8392
pft 11 / 131
[4645] ++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++ 8419
pft 11 / 150
[4704] ++GGGG+GGGGGG+++G+++G+GGGGG+GG++G+G++G+G+GGG+GGG+++++++GGG++ 8424
pft 7 / 99
[4732] +GG+GGG+G++GG+G+++G++++++++G++G+G+++++++++++++++++++++++++++ 8433
pft 23 / 151
[4779] ++++++++++G++++a++G++++++++++++G+aG++++++++G++++++++++++++++ 8439
pft 30 / 165
[4832] ++++++++a+++++G+++++Ga++++G++++G++G++GG+G++++++++++++G+G++a+ 8446
pft 29 / 145
[4879] +++++++++++++++++++++a++++++++++++++++++++a++++a++++++++++++ 8451
pft 36 / 123
[4936] +++++++++++++++++++++a+++++++++++a++++++++++++++++++a+++++++ 8458
pft 30 / 104
[4992] G+G+++++++++++++++++++++++++++++++++++++++++++++G+++++++++++ 8460
pft 17 / 158
[5050] ++++++++++++++GG++++++++++G++++++G+++Ga++++G++GG+G+G++++++GG 8469
pft 25 / 145
[5096] GG++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++ 8815
pft 13 / 118
[5154] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8902
pft 12 / 122
[5214] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8937
pft 17 / 143
[5274] +++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++ 8948
pft 20 / 149
[5333] +++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++ 9001
pft 17 / 152
[5392] ++++++++++++++++++++++++++++a+++GGGGGGGG++GGGGGGGGGa++++++++ 9015
pft 20 / 131
[5433] +++++++++++G++G++++G+G+GG++++++++G+G++GG+GGG++++++G++G+GG+G+ 9086
pft 11 / 128
[5474] GGGG+G++++++++GG++++++++++++++++++++++++++++++++++++++++++++ 9224
pft 12 / 125
[5528] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9236
pft 18 / 144
[5588] ++++++++++++++++G+++++++++++++++++++++++++++++G++++GGGG+G+++ 9248
pft 17 / 153
[5641] ++++++G++++++++++++++++++++++++++++++GGG+++++++G++++++++++++ 9385
pft 14 / 124
[5696] ++G++++++++G+++++GG+++++++++++G+GG++++++++++++G+++++++++++++ 9402
pft 16 / 144
[5748] +GG++++++++++++G++++G++++++++++++++++G++++++++++++++G++++++G 9411
pft 18 / 148
[5800] G+G+++++G+G++++++G++++GGa++G++++++G++G++++a++G+++++++GGGGG+G 9411
pft 23 / 116
[5842] +++++++++++++++++++GG++G+++aG++++G++GG+++G++++++++++++++++++ 9416
pft 34 / 126
[5893] +++++G++G+GG+++++++a++++++++GG+++++++++G++++++++++++++++++++ 9424
pft 41 / 133
[5945] ++++++G++++++++++++++Ga+G+++G++G++GG+++++G+++G+++G+G++++++++ 9426
pft 43 / 93
[5993] +++++a+++++G+++++G++a++++++G++++++++++++++++++++G+++++++++GG 9427
pft 46 / 86
[6045] +++G++++++GG++++++++++G++G++++GG+++++++++++++++++GG+++++++++ 9435
pft 54 / 88
[6096] +++G++++++GGGGGGGGGGGG+++++++GGGGGGGGGGGGGG+++++++++a+++++++ 9441
pft 28 / 72
[6128] +++++++GGGGGG+++GGG++G+++GG+++++++G+GG+G++++++++++++GG+++G+G 9441
pft 52 / 59
[6167] aaaaaaaa+aaaadaa++a++aaaaaaaa++d+aaaaaaaaGaGaaaGaaGaaGGGGGGG 9443
pft 229 / 130
[6175] GGGGGGGaGaaaaaaa++++++++++++++++++++++++++++++++++++++++++++ 9444
pft 20 / 157
[6220] ++++++++++++++++++++a++a+++a+aaaaaaaaa+++++++dGGG+G+GaGGG+GG 9449
pft 84 / 160
[6255] GGGaGGGGGaaGaGGGGGGGGGaGGaGaGGGGGGGGaGaGGGGaGGGaGGGGGaGGGGGG 9449
pft 38 / 102
[6255] GGGGGGGGGGGGGGGGGGGGGGGGaaGGGGGaGaa+GGGGGGGGGGGGGGGGpriv_ld addRead:
875503
priv_ld total: 1000310
Timing BFC paf construct: 1000366

ccon timings:
cct pre 5008
cct dir 8647
cct xcu 33106
cct tmp 3581
cct sw 542735
cct pic 3456
cct ico 225687
cct icm 0
cct upd 4006
cct del 0
cct rmz 3802
cct gcp 1963

ccon i timings (6255):
ccit insglcc 302
ccit insglaro 856
ccit insglact 104
ccit insgltot 5262
ccit pr 40856
ccit templ 6217
ccit index 3431
ccit biglccins 6791
ccit biglinterpol 1177
ccit biglupdtags 704
ccit biglfpcri 660
ccit bigllgap 38888
ccit biglshiftread 6165
ccit bigltot 101512
ccit insgr 3502
ccit ucv 34388

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 6256
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:11 2015
Timing BFC analysereadcov: 29119
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 202
mict_fallout 11649
mict_newin 5123
mict_helper1 52567
mict_newin 5123
mict_restofloop 5176
mict_totalloop 94901
done.

-------------- Contig statistics ----------------
Contig id: 25
Contig length: 9449

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 6256 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 268 0 0
0 0 0
Avg. coverage 0.000 0.000 128.139 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 268
Avg. contig coverage: 128.139

Consensus contains: A: 1441 C: 2658 G: 2539 T: 1536 N: 0
IUPAC: 0 Funny: 0 *: 1275
GC content: 63.580%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 96327
Localtime: Mon Jun 15 17:09:11 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 137603 cases.

P 1, marked 137603 reads.
Timing BFC edit tricky1: 84643
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)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 86590
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 643 positions.
Localtime: Mon Jun 15 17:09:12 2015
Deleting superfluous gap columns (2) ... done, deleted 171 columns.
Localtime: Mon Jun 15 17:09:12 2015
Timing BFC edit single discrepancy, no HAF: 89550
bfc 12/0
Timing BFC delPSHP: 1633
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: 674
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 599
mict_pre 7
mict_shadow 198
mict_fallout 11465
mict_newin 5090
mict_helper1 52459
mict_newin 5090
mict_restofloop 5123
mict_totalloop 94149
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 279477
Contig coverage analysis ... Timing BFC loop total: 1673678
bfc 1
Localtime: Mon Jun 15 17:09:12 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 26
Localtime: Mon Jun 15 17:09:12 2015
Unused reads: 1596249
bfc 8/0
0 Known 1: 6256
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 406
pft 11 / 122
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 688
pft 11 / 117
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 790
pft 16 / 142
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1107
pft 11 / 130
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1250
pft 13 / 120
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1474
pft 10 / 118
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1579
pft 11 / 132
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1724
pft 15 / 134
[481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1884
pft 11 / 130
[541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2093
pft 10 / 124
[601] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 2196
pft 18 / 135
[660] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 2437
pft 14 / 122
[719] +++++++++++++++++++++++++++++a+++++++a++++++++++++++a+++++++ 2479
pft 17 / 129
[776] +++++++++++++a++++++++++++++++d+++++++++++++++++++++++++++++ 2522
pft 18 / 117
[834] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 2536
pft 22 / 135
[893] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++aa+ 2558
pft 24 / 102
[951] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2572
pft 22 / 95
[1011] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2611
pft 22 / 93
[1071] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2617
pft 23 / 76
[1131] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2636
pft 20 / 77
[1190] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2981
pft 12 / 111
[1250] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++d++ 3084
pft 14 / 123
[1309] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3169
pft 19 / 82
[1369] ++++++++++++++++++++++++++++++a+++++a+++++++++++++a+++++++++ 3223
pft 17 / 76
[1426] ++a++a++a+a+a+++++++++++++++++++++++++++++++++a+++++++++++++ 3308
pft 15 / 123
[1480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3659
pft 19 / 126
[1540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3930
pft 11 / 117
[1600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4052
pft 13 / 129
[1660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4063
pft 19 / 134
[1720] +++++a+++++++++++++++++++++++++a++++++++++++++++++++++++++++ 4079
pft 17 / 100
[1778] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4088
pft 13 / 108
[1838] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4105
pft 12 / 124
[1898] +++++++++++++++++++++++++++++++++++++++a+a+++++++a++a+++++++ 4121
pft 19 / 124
[1954] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4130
pft 18 / 159
[2014] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4135
pft 31 / 101
[2074] +++++++++++++++++aaaaaaaaaaaaaaaaa+aaaaa+aaaaaaaaaaaaapriv_ld addRead:
255747
priv_ld total: 287560
Timing BFC paf construct: 287645

ccon timings:
cct pre 1627
cct dir 2036
cct xcu 7029
cct tmp 1157
cct sw 155209
cct pic 1185
cct ico 71030
cct icm 0
cct upd 1299
cct del 0
cct rmz 1263
cct gcp 215

ccon i timings (2091):
ccit insglcc 221
ccit insglaro 803
ccit insglact 97
ccit insgltot 2704
ccit pr 13350
ccit templ 1782
ccit index 1100
ccit biglccins 2030
ccit biglinterpol 447
ccit biglupdtags 255
ccit biglfpcri 229
ccit bigllgap 11637
ccit biglshiftread 2449
ccit bigltot 29725
ccit insgr 1192
ccit ucv 10955

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2092
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:12 2015
Timing BFC analysereadcov: 9208
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 64
mict_fallout 4339
mict_newin 2254
mict_helper1 17500
mict_newin 2254
mict_restofloop 2306
mict_totalloop 35440
done.

-------------- Contig statistics ----------------
Contig id: 26
Contig length: 4136

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2092 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 201 0 0
0 0 0
Avg. coverage 0.000 0.000 93.269 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 201
Avg. contig coverage: 93.269

Consensus contains: A: 710 C: 1131 G: 1243 T: 581 N: 0
IUPAC: 0 Funny: 0 *: 471
GC content: 64.775%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 35927
Localtime: Mon Jun 15 17:09:12 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 39935 cases.

P 1, marked 39935 reads.
Timing BFC edit tricky1: 24266
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 26310
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 229 positions.
Localtime: Mon Jun 15 17:09:12 2015
Deleting superfluous gap columns (2) ... done, deleted 74 columns.
Localtime: Mon Jun 15 17:09:12 2015
Timing BFC edit single discrepancy, no HAF: 27039
bfc 12/0
Timing BFC delPSHP: 281
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: 150
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 124
mict_pre 5
mict_shadow 58
mict_fallout 4300
mict_newin 2284
mict_helper1 16974
mict_newin 2284
mict_restofloop 2243
mict_totalloop 34748
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 89388
Timing BFC loop total: 501469
bfc 1
Localtime: Mon Jun 15 17:09:12 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 27
Localtime: Mon Jun 15 17:09:12 2015
Unused reads: 1594157
bfc 8/0
0 Known 1: 2092
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 364
pft 12 / 116
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 603
pft 12 / 117
[121] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 779
pft 16 / 140
[180] +++++++++++++++++++++++++++++++a+++++++a+a++++++++++++++++++ 1040
pft 11 / 127
[237] ++++++++++++++++++++a++a++++++++++a+++++++++a+++++++++++++++ 1159
pft 13 / 117
[293] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1478
pft 11 / 119
[353] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1669
pft 11 / 118
[413] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1716
pft 15 / 139
[473] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 1818
pft 15 / 128
[531] a++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 1935
pft 17 / 110
[590] +++++++++++++a+++++++++++a++++++++++++++++++++++++++++++++++ 2050
pft 16 / 109
[648] +++++++++++++++++++++++++++++++++++++++++++++++aa+++++++++++ 2195
pft 10 / 123
[706] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 2231
pft 16 / 105
[765] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2417
pft 14 / 116
[825] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2627
pft 10 / 116
[885] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2740
pft 15 / 148
[945] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2944
pft 14 / 121
[1005] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3014
pft 16 / 127
[1065] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3048
pft 20 / 126
[1125] +++++++++++++++++++++++++++++++a++++++++++++a+a+++a+++++++++ 3122
pft 20 / 116
[1181] ++++++a+++++++++++++++++++++++++++++++++++a+++++++++++++++++ 3151
pft 18 / 110
[1239] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 3183
pft 18 / 95
[1298] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3360
pft 17 / 103
[1358] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3550
pft 11 / 126
[1418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3820
pft 12 / 123
[1478] +++++++++++a+++++++++++++++++++a+++++++++++a+a++++++++++++++ 3854
pft 14 / 121
[1534] ++++++++++++++++++++++++++++a+a+++++++++++++++++++++++++++++ 3971
pft 11 / 121
[1592] +++++++++++a++++++++++++++++++++++a+++++++++++++++++++++aa++ 4020
pft 15 / 136
[1648] ++++++++a++++++a+++++++++++++++++++++++++++++a++++++++++++++ 4035
pft 16 / 97
[1705] ++++++++++++++++++++++a++++a+++++++++++++++a++++++++++++++++ 4071
pft 21 / 101
[1762] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4079
pft 19 / 90
[1822] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4102
pft 20 / 81
[1882] +++++++++++a+++++++++++++++++++++a+++++++++a++++++++++++++++ 4118
pft 19 / 78
[1939] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 4429
pft 15 / 97
[1998] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4632
pft 11 / 125
[2058] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4710
pft 17 / 132
[2117] a+++++++++++++++++++++++++a+a+++++++++++++++++++++++++++++++ 4916
pft 14 / 117
[2175] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4945
pft 12 / 101
[2235] +++++++++++++++++++++++++++++++++a++++++++++++++++++a+++a+++ 4968
pft 13 / 95
[2292] ++++++++++++++++++++++++++++++++++++++++a+++a+++++++++++++++ 5092
pft 13 / 122
[2350] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5376
pft 11 / 118
[2410] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5400
pft 17 / 133
[2470] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5758
pft 11 / 110
[2530] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5839
pft 15 / 119
[2590] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 5906
pft 14 / 126
[2649] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6039
pft 15 / 92
[2709] +++a+++++++++++++++++++++aaaa+++++++++++++++++++++++++++++++ 6054
pft 15 / 136
[2764] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6197
pft 10 / 131
[2824] +++++++++++++++++++++++++++++++++++++++++++++++++++aa+++++++ 6321
pft 10 / 133
[2882] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6343
pft 18 / 146
[2942] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6354
pft 17 / 149
[3002] ++++++++++++++++++++++++++++++++++++++++++++++++++++Ga+G++++ 6365
pft 15 / 137
[3059] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++GGG 6377
pft 15 / 153
[3116] ++G++++++G++G+++++++++++++++++++++++++++++++++++++++++++++++ 6382
pft 19 / 119
[3173] +++++GGG++GG+G++GG++GG+GG+GG+++GGGGG+GG++++++++GGG++G+++G+++ 6384
pft 9 / 109
[3207] +G++++G++++aG+++++G+G++GGG++++++++GG++++++++++++++++++++++GG 6393
pft 12 / 122
[3253] G++G+GGGGGG+++++++++++++++++++++++++++++++++++++++++++++++++ 6399
pft 17 / 140
[3306] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 6406
pft 33 / 137
[3365] ++++++++++a+++++++++++++++++++GG+++++++G++++++++++++++++++++ 6421
pft 23 / 130
[3420] G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6891
pft 15 / 122
[3480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7115
pft 12 / 124
[3540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7152
pft 13 / 139
[3600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7183
pft 15 / 135
[3660] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 7226
pft 17 / 125
[3719] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7268
pft 21 / 133
[3779] ++++++a++++++++++++++++++++++a++++++++a+++++++++++++++++++++ 7345
pft 17 / 110
[3836] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7588
pft 11 / 125
[3896] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7736
pft 11 / 126
[3956] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7765
pft 10 / 136
[4016] +++++++++++a++++++++++++++++++++++++++++++++++++++++++++++++ 7904
pft 8 / 142
[4075] ++++++++a+d+++++++d+++++++++++++++++++++++++++++++++++++++++ 7930
pft 12 / 146
[4132] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7945
pft 18 / 152
[4192] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 8168
pft 16 / 115
[4251] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8201
pft 11 / 120
[4311] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8350
pft 9 / 135
[4371] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8748
pft 15 / 158
[4431] ++++++++++++++++++++++++++++++++++++++++++++G++++G++++++++++ 8998
pft 12 / 134
[4489] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9265
pft 10 / 119
[4549] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9343
pft 11 / 125
[4609] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9592
pft 10 / 126
[4669] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9748
pft 10 / 119
[4729] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9949
pft 12 / 130
[4789] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9991
pft 14 / 134
[4849] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10013
pft 20 / 132
[4909] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10030
pft 22 / 126
[4969] ++++++++++++++++++++++a++++++++++++++++++++++++++++++++++a++ 10047
pft 17 / 111
[5027] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10286
pft 18 / 90
[5087] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10403
pft 13 / 147
[5147] +++++++++++++aa+++++++++++++++++++++++++++++++++++++++++++++ 10588
pft 12 / 117
[5205] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10869
pft 11 / 122
[5265] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10973
pft 14 / 121
[5325] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11100
pft 12 / 123
[5385] ++++++++++++++++++++++a+++++++++++a+++++++++++++++++++++++++ 11109
pft 11 / 129
[5443] +++++++a++a+++++++++++++++++++++++++++++++++++++++++++++++++ 11121
pft 14 / 145
[5501] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11126
pft 16 / 125
[5561] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11131
pft 13 / 134
[5621] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 11136
pft 15 / 131
[5680] ++++++++++++++++++++++++++a++++++++++++++++++++++++a++++++++ 11139
pft 14 / 141
[5738] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 11147
pft 17 / 150
[5797] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 11158
pft 42 / 175
[5856] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11163
pft 20 / 146
[5916] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 11166
pft 16 / 151
[5975] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11175
pft 19 / 165
[6035] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 11189
pft 28 / 163
[6094] ++++++++++++a++++++++++++++++++++++++++++++a+a++++++++++++++ 11199
pft 36 / 138
[6151] +++++++++++++++++++++++++++a++++++++++++++++a+++++++++++++++ 11209
pft 32 / 115
[6209] +++++++++++++++++++++++++++++++++++++++G++GG++++++++++++++++ 11211
pft 22 / 123
[6266] ++++++++++G+++++++++++++++++++++++Ga+++++GG+++++G+a+++++++++ 11216
pft 14 / 148
[6319] +++a+++G+++++GGGGG+G++++++Ga++G++G+++G+++G+++G+G++++++G+G++a 11220
pft 27 / 142
[6360] +G++G+++++++++GGGGGGGG+G+G+GaGG+G+++GG++G++G+GGGG+++G++++GGG 11222
pft 31 / 88
[6391] +Ga+a+G+++++++aG+G+G+++++Ga+++++++++++G+GGa+++++GGGG+G+GGGG+ 11228
pft 36 / 82
[6428] +G++++++++++++++++GGGGGGG+++GGGG++GG+G+G+GGGGGGG+aaaaaaaaaaa 11230
pft 161 / 69
[6453] aa+++aaaaaaaa+aaaaaaaaaa+aaaaaaaaaaaa+aa+a+++++aaaa+a++a++++ 11234
pft 5 / 129
[6473] ++++aa+++++++aaaaaa++G++++++++++++++++++++G+Ga+a++a+GGG+a+G+ 11237
pft 47 / 156
[6513] aGGGaGGGGGG+GGGGaG+GGGGGGGGGGGGGGGaGaGGGGGGGGGGGGGGaaaGGaaGG 11238
pft 16 / 87
[6515] GGGGGGaa+aGGGGGGGGGGGGGGGGGGapriv_ld addRead: 878489
priv_ld total: 986040
Timing BFC paf construct: 986092

ccon timings:
cct pre 5061
cct dir 8499
cct xcu 31718
cct tmp 3696
cct sw 540038
cct pic 3601
cct ico 232192
cct icm 0
cct upd 4130
cct del 0
cct rmz 4008
cct gcp 1425

ccon i timings (6515):
ccit insglcc 508
ccit insglaro 1626
ccit insglact 197
ccit insgltot 6950
ccit pr 42468
ccit templ 6478
ccit index 3502
ccit biglccins 6362
ccit biglinterpol 1305
ccit biglupdtags 750
ccit biglfpcri 675
ccit bigllgap 39629
ccit biglshiftread 7030
ccit bigltot 101711
ccit insgr 3621
ccit ucv 35760

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 6516
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:13 2015
Timing BFC analysereadcov: 29811
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 9
mict_shadow 205
mict_fallout 12869
mict_newin 6155
mict_helper1 55186
mict_newin 6155
mict_restofloop 6240
mict_totalloop 104584
done.

-------------- Contig statistics ----------------
Contig id: 27
Contig length: 11238

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 6516 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 218 0 0
0 0 0
Avg. coverage 0.000 0.000 112.077 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 218
Avg. contig coverage: 112.077

Consensus contains: A: 1791 C: 3123 G: 3210 T: 1719 N: 0
IUPAC: 0 Funny: 0 *: 1395
GC content: 64.340%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 106145
Localtime: Mon Jun 15 17:09:14 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 139367 cases.

P 1, marked 139367 reads.
Timing BFC edit tricky1: 86172
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 90542
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 719 positions.
Localtime: Mon Jun 15 17:09:14 2015
Deleting superfluous gap columns (2) ... done, deleted 229 columns.
Localtime: Mon Jun 15 17:09:14 2015
Timing BFC edit single discrepancy, no HAF: 99506
bfc 12/0
Timing BFC delPSHP: 1699
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: 446
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 675
mict_pre 7
mict_shadow 184
mict_fallout 12589
mict_newin 6098
mict_helper1 53888
mict_newin 6098
mict_restofloop 6130
mict_totalloop 102148
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 291995
Contig coverage analysis ... Timing BFC loop total: 1697552
bfc 1
Localtime: Mon Jun 15 17:09:14 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 28
Localtime: Mon Jun 15 17:09:14 2015
Unused reads: 1587641
bfc 8/0
0 Known 1: 6516
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 432
pft 12 / 125
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 656
pft 11 / 124
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 728
pft 12 / 128
[181] ++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++a 748
pft 15 / 150
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1077
pft 12 / 119
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1224
pft 14 / 120
[359] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+a 1273
pft 15 / 126
[417] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1426
pft 14 / 112
[477] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1563
pft 13 / 108
[537] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1991
pft 11 / 120
[597] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2167
pft 13 / 129
[657] ++a++++++a++++++++++a+++++++++a+++++++++++++++++++++++++++++ 2303
pft 14 / 125
[712] a++++++++++++++++++++++a++++++++++++++++++++++++++++aa++a+++ 2319
pft 14 / 121
[768] ++++++++++++++++++++++++++++++++a++++++++++++a++++++aa++++++ 2337
pft 15 / 114
[823] aa++++++++++++a++++++++++++++++++++a+++++a++++++++a+++++a+++ 2384
pft 13 / 115
[877] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 2409
pft 15 / 116
[936] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2452
pft 19 / 123
[995] +++++++++++++++++++a+++++++++++++++++++++++++++++++a++a++aa+ 2501
pft 13 / 136
[1050] +++++++++++++++a++++++++++++++a+++a+a+++++++++++++++++++++++ 2532
pft 11 / 130
[1106] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2864
pft 11 / 119
[1166] +++++++++++++++++++++++++++++++a+++++++a++++++++++++++++++++ 2948
pft 15 / 123
[1224] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3138
pft 12 / 131
[1284] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3156
pft 18 / 118
[1344] ++++++++++++++a++++++++++++++++++++++++++++++++++++++++a++++ 3178
pft 16 / 110
[1402] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3320
pft 16 / 92
[1462] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3467
pft 11 / 117
[1522] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3542
pft 11 / 138
[1582] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 3655
pft 16 / 156
[1641] ++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 3666
pft 10 / 158
[1700] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3672
pft 10 / 148
[1760] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3683
pft 15 / 175
[1820] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3691
pft 24 / 157
[1880] +++++++++++++++++++++++++++++++++++++a++++++++++++++++++++++ 3704
pft 23 / 144
[1939] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 3711
pft 23 / 133
[1998] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3712
pft 19 / 115
[2058] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3713
pft 18 / 159
[2118] ++++++++++++++++++++++a++++++++++a++++a+++++++++++++++++++++ 3760
pft 33 / 149
[2175] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3764
pft 19 / 168
[2235] ++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++G+ 3772
pft 26 / 130
[2293] +GG++++++G+G++++++G++G+++GG+G+G++GG+GG++GG+++++G+GGGG+G+GG++ 3779
pft 12 / 130
[2328] G+GGG+G++G+G++GGG+++++++++G+GGGG+G+++GG+GG++GGGGGGGG+G+G++GG 3782
pft 16 / 94
[2357] +G+G+G+GG+G++GGGGGG+GGGG++G++G++G++G++G++GG++GGGG+G+GGGG+G+G 3783
pft 23 / 72
[2382] G+G++GGGG+a+a+aaaaaaaaaaaaaaaaaaa+aaaaaaaaaaa+GGGGGGGGGGGGGG 3797
pft 63 / 96
[2390] GGGGG+GGGGGGGGGGGGGGGGG+GGGG+GGGGGGGGGGGGGGGGGGG+GGG+aaaaaaa 3798
pft 43 / 90
[2395] aaaGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG+GGGGG 3798
pft 25 / 87
[2396] GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 349037
priv_ld total: 392846
Timing BFC paf construct: 392923

ccon timings:
cct pre 2018
cct dir 2750
cct xcu 14571
cct tmp 1492
cct sw 218481
cct pic 1354
cct ico 87467
cct icm 0
cct upd 1527
cct del 0
cct rmz 1470
cct gcp 918

ccon i timings (2395):
ccit insglcc 216
ccit insglaro 640
ccit insglact 71
ccit insgltot 2625
ccit pr 15226
ccit templ 2084
ccit index 1290
ccit biglccins 2544
ccit biglinterpol 485
ccit biglupdtags 266
ccit biglfpcri 236
ccit bigllgap 14081
ccit biglshiftread 2821
ccit bigltot 40040
ccit insgr 1313
ccit ucv 13230

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2396
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:15 2015
Timing BFC analysereadcov: 10959
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 80
mict_fallout 4633
mict_newin 2088
mict_helper1 20692
mict_newin 2088
mict_restofloop 2161
mict_totalloop 37869
done.

-------------- Contig statistics ----------------
Contig id: 28
Contig length: 3798

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2396 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 224 0 0
0 0 0
Avg. coverage 0.000 0.000 122.209 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 224
Avg. contig coverage: 122.209

Consensus contains: A: 582 C: 1036 G: 1078 T: 580 N: 0
IUPAC: 0 Funny: 0 *: 522
GC content: 64.530%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 38371
Localtime: Mon Jun 15 17:09:15 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 53779 cases.

P 1, marked 53779 reads.
Timing BFC edit tricky1: 31077
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: 34123
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 153 positions.
Localtime: Mon Jun 15 17:09:15 2015
Deleting superfluous gap columns (2) ... done, deleted 48 columns.
Localtime: Mon Jun 15 17:09:15 2015
Timing BFC edit single discrepancy, no HAF: 29470
bfc 12/0
Timing BFC delPSHP: 475
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: 532
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 149
mict_pre 6
mict_shadow 73
mict_fallout 4440
mict_newin 2033
mict_helper1 19358
mict_newin 2033
mict_restofloop 2090
mict_totalloop 35821
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 108145
Timing BFC loop total: 647499
bfc 1
Localtime: Mon Jun 15 17:09:15 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 29
Localtime: Mon Jun 15 17:09:15 2015
Unused reads: 1585245
bfc 8/0
0 Known 1: 2396
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 612
pft 11 / 112
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 778
pft 13 / 122
[121] +++++++++++++++++a+++++a++++++++++++++++++++++a+++++++++++++ 867
pft 11 / 118
[178] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 941
pft 17 / 118
[238] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1195
pft 15 / 114
[298] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1468
pft 10 / 115
[358] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1569
pft 12 / 129
[418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1631
pft 15 / 132
[478] +++++++++++++++++++++++++++++++++++++++a++++++++++++++a+++++ 1717
pft 19 / 131
[536] +++a++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 1738
pft 20 / 109
[594] ++++++++++++++++++++++++++++a++++++++++++++a++++++++++++++++ 1747
pft 22 / 116
[652] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 1817
pft 21 / 93
[711] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2084
pft 11 / 98
[771] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2439
pft 10 / 112
[831] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2566
pft 11 / 123
[891] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2712
pft 11 / 120
[951] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2747
pft 17 / 122
[1011] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2807
pft 18 / 118
[1071] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 2815
pft 19 / 97
[1130] +++++++++++++++++++++++a+++++++++++++++++++a+++++++++++++++a 2840
pft 22 / 88
[1187] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 2861
pft 19 / 89
[1246] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2864
pft 23 / 75
[1306] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 2872
pft 20 / 72
[1365] +++++++++++++++++++++++++a++++++++++++++++++++++++++++++++++ 2911
pft 21 / 66
[1424] +++++++++++++++++++++++++a+++++++++++aa+++++++++++++++++++++ 3045
pft 17 / 85
[1481] +a+a+++++++a++a++++++++++++++++a++++a+++++aa+a++a+++++a+++++ 3171
pft 18 / 146
[1530] ++++++++++++++++++++aa++++++a++++++++++a++++++++a+++++++a+a+ 3175
pft 12 / 135
[1582] a++a+++a+a+++++++++++++a++++a+aa++++aa+a++++++++++++++++aa++ 3311
pft 12 / 126
[1629] a++++++a+a+++a+a++a++++++++a++++++++++++a++++++++++++a++a+++ 3317
pft 17 / 106
[1680] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3350
pft 22 / 116
[1740] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3358
pft 19 / 136
[1800] ++++++++++++++++++++++++++++++++GGGG++GG++GGGG++G+GG++G++GG+ 3365
pft 21 / 111
[1844] ++GG+GGG+G++GGGGG+G+GG+++GG+GGGa+GGGG+GG+GGGGGGG+GG+GGG++GG+ 3368
pft 13 / 86
[1863] GGGGGGGGGG++G++GGG+GGG+GGGGGGGGGGG++GGGGGGGGG+GG+G++Gaaaaaaa 3368
pft 69 / 64
[1875] aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaGGGGGGGGGGGGGGGGGaGGGG 3368
pft 3 / 106
[1875] GGGGGGGGGGGGGGGGGGGGGGGGGG+aaaaGGGGGGGGGGGGGGGpriv_ld addRead: 237061
priv_ld total: 272147
Timing BFC paf construct: 272207

ccon timings:
cct pre 1559
cct dir 2854
cct xcu 6813
cct tmp 1189
cct sw 150184
cct pic 1006
cct ico 57170
cct icm 0
cct upd 1116
cct del 0
cct rmz 1106
cct gcp 799

ccon i timings (1875):
ccit insglcc 13
ccit insglaro 53
ccit insglact 6
ccit insgltot 1176
ccit pr 11250
ccit templ 1531
ccit index 1017
ccit biglccins 1423
ccit biglinterpol 332
ccit biglupdtags 195
ccit biglfpcri 190
ccit bigllgap 8346
ccit biglshiftread 1370
ccit bigltot 22372
ccit insgr 1111
ccit ucv 9593

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1876
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:15 2015
Timing BFC analysereadcov: 8020
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 6
mict_shadow 54
mict_fallout 3724
mict_newin 1894
mict_helper1 15292
mict_newin 1894
mict_restofloop 1934
mict_totalloop 30178
done.

-------------- Contig statistics ----------------
Contig id: 29
Contig length: 3368

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1876 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 180 0 0
0 0 0
Avg. coverage 0.000 0.000 99.664 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 180
Avg. contig coverage: 99.664

Consensus contains: A: 596 C: 898 G: 994 T: 517 N: 0
IUPAC: 0 Funny: 0 *: 363
GC content: 62.962%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 30575
Localtime: Mon Jun 15 17:09:15 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 31578 cases.

P 1, marked 31578 reads.
Timing BFC edit tricky1: 19969
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 21975
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 641 cases.

Edited 641 reads.
Localtime: Mon Jun 15 17:09:15 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:15 2015
Timing BFC edit tricky2: 15373

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 151 positions.
Localtime: Mon Jun 15 17:09:15 2015
Deleting superfluous gap columns (2) ... done, deleted 212 columns.
Localtime: Mon Jun 15 17:09:15 2015
Timing BFC edit single discrepancy, no HAF: 33557
bfc 12/0
Timing BFC delPSHP: 237
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 9135
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 213
mict_pre 6
mict_shadow 58
mict_fallout 3336
mict_newin 1681
mict_helper1 13270
mict_newin 1681
mict_restofloop 1752
mict_totalloop 26705
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 66178
Timing BFC loop total: 478379
bfc 1
Localtime: Mon Jun 15 17:09:15 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 30
Localtime: Mon Jun 15 17:09:15 2015
Unused reads: 1583369
bfc 8/0
0 Known 1: 1876
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 440
pft 11 / 125
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 645
pft 12 / 134
[121] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 688
pft 14 / 131
[180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 917
pft 12 / 117
[240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1154
pft 10 / 117
[300] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 1200
pft 14 / 134
[359] +a+++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 1296
pft 15 / 128
[417] ++++++++++++++a++++++++++++a++++++++++++++++++++++++++++++++ 1343
pft 17 / 112
[475] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1376
pft 15 / 106
[535] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1838
pft 10 / 112
[595] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1941
pft 10 / 123
[655] ++++++++++++++a++a++++++++++++++++++++++++++++++++++++++++++ 2143
pft 10 / 117
[713] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2427
pft 10 / 117
[773] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2520
pft 14 / 142
[833] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 2573
pft 17 / 137
[892] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 2609
pft 16 / 119
[951] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2636
pft 15 / 102
[1011] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2674
pft 15 / 98
[1071] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2939
pft 13 / 110
[1131] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3029
pft 14 / 115
[1191] ++++++++++++++++++++++a+++++++++++++++++++a+++++++++++++++++ 3161
pft 15 / 125
[1249] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3420
pft 11 / 119
[1309] +++++++++++++++++++++++++++++++++++aaa+a+aaaaa++++++++++++++ 3644
pft 10 / 119
[1360] +++++++a+++++++++++++++a+++++++++a++++++++++++++++++++++++a+ 3726
pft 11 / 122
[1416] ++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++ 3738
pft 11 / 123
[1475] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 3754
pft 13 / 137
[1534] ++++++++++++++++++++a++a+++++++++++++++++++++++a++++++++++++ 3769
pft 12 / 164
[1591] ++++++++++a+++++++++++++++++a+++++++++++++++++++++++++++++++ 3776
pft 20 / 152
[1649] +++++++++a+a+++++a++++++++++++++++++++++++++++++++++++++++++ 3778
pft 18 / 126
[1706] +++a++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3885
pft 25 / 153
[1765] +++++++++++++++++++++++++++++++++++++++++++++aa+++++++++++++ 3901
pft 39 / 127
[1823] ++++a+++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 3907
pft 26 / 100
[1881] ++++++++++++++++++++++++a+adaaaaaaaaaaaaaa+++dddaadaaaa+aaaa 3917
pft 12 / 137
[1909] aaa+++a++++aa++a+++++++++++++G++++++++++Ga+++++++a++++++++++ 3954
pft 18 / 136
[1959] ++++++++++a++a++GGGGGGGGGGGGGGGGG++G+++GGGGG+GG++++GGGG++a++ 3963
pft 16 / 103
[1987] +++++++aG++a++a++++GGG+a+++a++GaaaG++aa++++++G+G++++++++++++ 3966
pft 21 / 95
[2028] G+++++++++++++++++++G++++GGG+++++++++G++++++++++++++++a++aGG 3967
pft 24 / 173
[2079] ++++++++G+++GG++G+++++G+++++G+++++GG++++G+++G++G++++++a++++a 3969
pft 22 / 154
[2126] +++++++GG++a++++++G++++++++G+G++GG++++++a++aG+aa++++++G+++++ 3970
pft 18 / 153
[2171] aaa+aaaaaaaaaaaG++++G++G+++++GG+GG++GGG+G+++GGG+GG+G++G++GG+ 3974
pft 13 / 142
[2197] GGGa+GG+G+++G+G+++G+GG+++++dGG+++aG++d++Ga+a++G+GG+GG+++++GG 3975
pft 16 / 133
[2229] a+++a+++GG+aG+++a++G+d+++Ga++Ga+++G++++++++Ga++a++++a++aG+GG 3980
pft 16 / 144
[2268] +aaa+++aa+Ga+GGGGG+G++++a+++++++G+G++G++aG+Ga+GG+G+GG+a++aGG 3982
pft 17 / 130
[2297] G+G+GG+aa+GG+++G+++++GG+aG+Ga++G++GGa+Ga++++++++a+GGGG++GGGG 3984
pft 13 / 114
[2327] a++GG+a+++aGG++++++Ga++a+G+aG+a+a++Ga++G+++++G++G+G+++G+++++ 3988
pft 19 / 119
[2365] G++aG+a++++GGGG+a+++++++++G+++GGG++aG+GGa+a+G++a+++++G++a+G+ 3989
pft 19 / 110
[2402] ++GGG++++aaGaaaGGGa+aG++GGG+GG++G++G++GGGGGGGGGGGGGG++GGGa+a 3990
pft 9 / 91
[2421] ++G+++G+++G+G+++++G++GGG+++a+GG+G++++a+++++++G+G++a+++G++G++ 3992
pft 27 / 115
[2463] +a+G+aa+aaa++++aaaaaaaaaa+a++GGG+aGaGa++++++GGGGGGGGGGGGGGGG 3992
pft 13 / 95
[2481] ++G++++Ga++++Ga+a+++aa+G++a+++aG+a++G+aa++Gaaa+++GG+++aGGGG+ 3993
pft 20 / 93
[2514] +a+GG++++a+aaaaa+a++++aa++aaaaa++++GGGGGGGGGGGGG++++a++aa+G+ 3993
pft 14 / 84
[2540] +GGGGGGG+G++++++aa+++a+aaGa++GGG+GGGGGGGGGaa++a++++GGaa++aaa 3994
pft 12 / 80
[2563] ++a++GGGG++a++a++++G++a+aaaG+GGaaaaa+a++Gaa++a++++a+aa++++aa 3994
pft 21 / 85
[2592] aaaaa++G+++++++aaaaaaa+++aa++GGaa+aa+++++a++aa++Ga+++++++Gaa 3994
pft 22 / 83
[2624] +GGGGaGGaaaa++++++++aaaaaaaaaaaaaaa+aaaaaaaaaaaaaaaaaaaaaaaa 4020
pft 346 / 126
[2633] aaaaaa++GGGa+aGGaaa+aGGGGGGGGaGa+GGGGGGaaGa+GGa+GGGGGaGaaaa+ 4021
pft 11 / 118
[2642] +++G++++++G++G+++++++++G++GGGG++++++G+++++++GG++G+aGGGGG+GG+ 4022
pft 34 / 161
[2681] GG+++++GG+Gaa++G+GGGGG+GaGaG++G+GG++++G+GG++GGGGGGGa++G+GGG+ 4024
pft 27 / 156
[2706] +Ga+GGGGGGaGGGaGGa+aGaGGaaaGa+GGa++G+GG+GGGGaG+G+GGGGGGaaaGG 4024
pft 10 / 122
[2715] GaaGaGGGG+aaGG+GG+GGaa+GGG+GGaa++aGGGGaGG++GGGGa+GGGGG+GGG+G 4026
pft 17 / 118
[2728] +GGG+aGaGGa+++GGG+GGGGG+GGGGGa+GG+G+GGGaGGaGGGa+GG+GGGGGGGGa 4028
pft 10 / 110
[2739] GG+aGGGGGaaaaGaa+GGaaGa+aaGaaaaGaGG+GGaGGG++GG+GG+GGaGaaa+GG 4028
pft 17 / 109
[2748] GGGGG+aaaaG+GGGaaa+GGaaaaaaaaaaaaaaaaaaa+aGGGG+GGGa+GG+Ga+GG 4029
pft 17 / 110
[2756] GGGaaGaaGaGGaGGG+G+GGGaGGaG+GGGaaaaa+GGGGGGGGGG+GGGGa++GGGGG 4029
pft 16 / 83
[2763] Gaaaa+GGGGGGGGGGGGGaaGGaGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGGGG 4029
pft 286 / 115
[2764] GGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGaGG 4029
pft 5 / 129
[2764] GGGaGGGGGGGGGGGGGGaGGGGaGaGGGGGGGGGGGGGaGGGGaGGaaaaGGGaaaaaG 4029
pft 4 / 112
[2764] GGGGGGGGGaaGGaaaaaaaaaaaaGaaaaaaaaaaaaaaaaaGaaaGaGGGGGGGGGGG 4029
pft 133 / 116
[2764] GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGaaaGGGGGGGGGGaaGaaGGGGGGG 4029
pft 20 / 93
[2764] GGGGGGGGGGGGGGpriv_ld addRead: 510200
priv_ld total: 652027
Timing BFC paf construct: 652089

ccon timings:
cct pre 3042
cct dir 6122
cct xcu 18191
cct tmp 2230
cct sw 345436
cct pic 1545
cct ico 96412
cct icm 0
cct upd 1746
cct del 0
cct rmz 1693
cct gcp 9342

ccon i timings (2763):
ccit insglcc 51
ccit insglaro 155
ccit insglact 17
ccit insgltot 1917
ccit pr 17200
ccit templ 2530
ccit index 1505
ccit biglccins 2360
ccit biglinterpol 484
ccit biglupdtags 275
ccit biglfpcri 275
ccit bigllgap 15915
ccit biglshiftread 2198
ccit bigltot 43175
ccit insgr 1647
ccit ucv 15140

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2764
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:16 2015
Timing BFC analysereadcov: 12516
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 100
mict_fallout 4965
mict_newin 2145
mict_helper1 22912
mict_newin 2145
mict_restofloop 2192
mict_totalloop 40840
done.

-------------- Contig statistics ----------------
Contig id: 30
Contig length: 4029

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2764 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 488 0 0
0 0 0
Avg. coverage 0.000 0.000 131.396 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 488
Avg. contig coverage: 131.396

Consensus contains: A: 568 C: 1077 G: 1144 T: 720 N: 0
IUPAC: 0 Funny: 0 *: 520
GC content: 63.294%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 41323
Localtime: Mon Jun 15 17:09:16 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 60018 cases.

P 1, marked 60018 reads.
Timing BFC edit tricky1: 37406
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 5 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 40933
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 137 positions.
Localtime: Mon Jun 15 17:09:16 2015
Deleting superfluous gap columns (2) ... done, deleted 58 columns.
Localtime: Mon Jun 15 17:09:16 2015
Timing BFC edit single discrepancy, no HAF: 29755
bfc 12/0
Timing BFC delPSHP: 876
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: 876
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 162
mict_pre 7
mict_shadow 84
mict_fallout 4927
mict_newin 2158
mict_helper1 22675
mict_newin 2158
mict_restofloop 2130
mict_totalloop 40449
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 122992
Timing BFC loop total: 941260
bfc 1
Localtime: Mon Jun 15 17:09:16 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 31
Localtime: Mon Jun 15 17:09:16 2015
Unused reads: 1580605
bfc 8/0
0 Known 1: 2764
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 430
pft 11 / 114
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 630
pft 12 / 119
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 673
pft 15 / 120
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 904
pft 10 / 134
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 950
pft 14 / 126
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1063
pft 17 / 122
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1409
pft 14 / 109
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1479
pft 11 / 115
[481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1550
pft 16 / 122
[541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1764
pft 14 / 138
[601] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1794
pft 13 / 114
[661] +++++++++++a++++++++++++++++++++++++++++++++++++++++++++++++ 1824
pft 14 / 114
[720] ++++++++++++++++a+++++++++++++++++++++++++++++++++++a+++++++ 1847
pft 17 / 103
[778] +++++++++++++++++++++++++++++++++++a++aa++++a+a+++aaa+++++++ 2001
pft 12 / 107
[830] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2042
pft 10 / 118
[890] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 2097
pft 16 / 118
[949] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2469
pft 10 / 130
[1008] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2760
pft 10 / 126
[1068] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2786
pft 12 / 119
[1128] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3052
pft 13 / 114
[1188] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3557
pft 10 / 114
[1248] ++++++++++++++++a+++++++++++a++++a++++a++a+++a++a++++a+aa+++ 3569
pft 16 / 102
[1297] a++++aaaa+a++a++++++a+a+aaa++++++++++++++++++a++++++a+++++aa 3586
pft 15 / 88
[1342] +++aaaa++++++++++++++++++a++a+++++++++++++++++++++++++++++++ 3901
pft 13 / 109
[1396] +++++++++++++++++++++++++++++++aad++++++++++++++++++++++++++ 4037
pft 15 / 103
[1453] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4066
pft 10 / 135
[1513] ++aa++++++++++++++++++++++++++++++++++a++++++++a++++++++++++ 4073
pft 23 / 147
[1569] +++++++++aa++++a++++aaaaaa+a+a++++++++++++++a+a++aa+++++++a+ 4084
pft 19 / 106
[1613] ++++++++++++++++++++++++++++++++++++++++++aa++a+++++aaa+++++ 4090
pft 11 / 147
[1667] ++++++++++++++++++++++++++++a+++++++++a+++++++++++++++++++++ 4094
pft 25 / 150
[1725] ++++a+++++++++++++++++++++a+++++++a+++++++++++++++++++aaa+aa 4102
pft 62 / 118
[1776] aaaaaaaaa+aaaaaaaaaa+aaaapriv_ld addRead: 229133
priv_ld total: 255204
Timing BFC paf construct: 255326

ccon timings:
cct pre 1352
cct dir 1849
cct xcu 8890
cct tmp 959
cct sw 140906
cct pic 954
cct ico 59714
cct icm 0
cct upd 1079
cct del 0
cct rmz 1113
cct gcp 248

ccon i timings (1777):
ccit insglcc 154
ccit insglaro 468
ccit insglact 61
ccit insgltot 1967
ccit pr 10959
ccit templ 1470
ccit index 984
ccit biglccins 1801
ccit biglinterpol 402
ccit biglupdtags 220
ccit biglfpcri 195
ccit bigllgap 9178
ccit biglshiftread 2163
ccit bigltot 25346
ccit insgr 1038
ccit ucv 9433

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1778
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:17 2015
Timing BFC analysereadcov: 8057
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 57
mict_fallout 4061
mict_newin 2265
mict_helper1 15716
mict_newin 2265
mict_restofloop 2318
mict_totalloop 33315
done.

-------------- Contig statistics ----------------
Contig id: 31
Contig length: 4102

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1778 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 208 0 0
0 0 0
Avg. coverage 0.000 0.000 81.768 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 208
Avg. contig coverage: 81.768

Consensus contains: A: 592 C: 1221 G: 1200 T: 664 N: 0
IUPAC: 0 Funny: 0 *: 425
GC content: 65.842%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 33754
Localtime: Mon Jun 15 17:09:17 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 32761 cases.

P 1, marked 32761 reads.
Timing BFC edit tricky1: 21176
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 23015
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 600 cases.

Edited 600 reads.
Localtime: Mon Jun 15 17:09:17 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:17 2015
Timing BFC edit tricky2: 16307

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 172 positions.
Localtime: Mon Jun 15 17:09:17 2015
Deleting superfluous gap columns (2) ... done, deleted 265 columns.
Localtime: Mon Jun 15 17:09:17 2015
Timing BFC edit single discrepancy, no HAF: 36477
bfc 12/0
Timing BFC delPSHP: 244
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 9342
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 256
mict_pre 7
mict_shadow 55
mict_fallout 3645
mict_newin 2042
mict_helper1 13584
mict_newin 2042
mict_restofloop 2104
mict_totalloop 29547
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 73182
Timing BFC loop total: 478135
bfc 1
Localtime: Mon Jun 15 17:09:17 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 32
Localtime: Mon Jun 15 17:09:17 2015
Unused reads: 1578827
bfc 8/0
0 Known 1: 1778
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 418
pft 10 / 119
[61] ++++++++++++++a++a++++++++++++++a++++a++a++ad+++++++++++++++ 501
pft 13 / 122
[114] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 783
pft 12 / 115
[174] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 864
pft 13 / 133
[233] a++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 1095
pft 13 / 122
[292] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1315
pft 10 / 127
[352] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1527
pft 14 / 119
[412] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1646
pft 14 / 123
[472] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 1755
pft 19 / 118
[531] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1914
pft 19 / 110
[591] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2035
pft 11 / 127
[651] +++++++++++++++++++++++++++++++++++++++++++++a+a+a++++++++++ 2112
pft 19 / 128
[708] +++++++++++++++++++++++++++a++++++++++a+++++++++++++++++++++ 2270
pft 18 / 115
[766] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2542
pft 8 / 117
[826] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2577
pft 13 / 123
[886] ++++++++++++++++++++d+++++++++++++++++++++++++++++++++++++++ 2581
pft 19 / 98
[945] ++++++++++++++++++++a+++++++a++++++++++++++++++++a++++++++++ 2587
pft 16 / 91
[1002] ++++++++++++++++++++++a+++++++++++++++++a++a++++++++++++++++ 2922
pft 20 / 120
[1059] +++++++++++d++++++++++++++++++++++++++++++++++++++++++++++++ 3272
pft 10 / 109
[1118] +++++a++a++++++++++++++++++++++++a+aa+++a++++a+++daaaaa+++++ 3474
pft 8 / 122
[1165] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3821
pft 10 / 117
[1225] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3863
pft 13 / 120
[1285] ++++++++++++++++++++++++++a+++a+++++++++++++++++++++++++++++ 4147
pft 11 / 112
[1343] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4440
pft 11 / 117
[1403] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4674
pft 14 / 139
[1463] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4963
pft 12 / 121
[1523] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5051
pft 13 / 118
[1583] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 5061
pft 14 / 108
[1642] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5316
pft 12 / 117
[1702] +++++++a++++a+++++++++++++++++++++++++++++++++++++++++++++++ 5332
pft 15 / 109
[1760] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5341
pft 21 / 91
[1820] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 5352
pft 17 / 83
[1879] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 5426
pft 16 / 85
[1938] +++++++++++++++++a+++++++++++++++aa+++++++++++++++++++++++++ 5681
pft 17 / 108
[1995] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5827
pft 11 / 120
[2055] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6016
pft 12 / 114
[2115] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6150
pft 18 / 89
[2175] +++++++++++++++++++++++++++a++a+++++aaaa++++++++++++++++++++ 6183
pft 17 / 132
[2229] ++++++++++++++++++++++++a++++++++++++++a+a++++++++++++++++++ 6188
pft 26 / 156
[2286] ++++++a+++++++a+++++++++aa+++++++++++++a+ddaadaaaaadaaaaa+aa 6196
pft 45 / 110
[2322] aaaaaaaaaaaaaaaaaapriv_ld addRead: 286076
priv_ld total: 319006
Timing BFC paf construct: 319064

ccon timings:
cct pre 1730
cct dir 2116
cct xcu 8485
cct tmp 1317
cct sw 174431
cct pic 1279
cct ico 78191
cct icm 0
cct upd 1469
cct del 0
cct rmz 1390
cct gcp 285

ccon i timings (2321):
ccit insglcc 374
ccit insglaro 1189
ccit insglact 146
ccit insgltot 3616
ccit pr 14787
ccit templ 1948
ccit index 1227
ccit biglccins 2493
ccit biglinterpol 536
ccit biglupdtags 324
ccit biglfpcri 296
ccit bigllgap 11120
ccit biglshiftread 3199
ccit bigltot 31803
ccit insgr 1268
ccit ucv 12117

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2322
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:17 2015
Timing BFC analysereadcov: 10544
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 79
mict_fallout 5464
mict_newin 3249
mict_helper1 19700
mict_newin 3249
mict_restofloop 3428
mict_totalloop 45175
done.

-------------- Contig statistics ----------------
Contig id: 32
Contig length: 6196

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2322 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 166 0 0
0 0 0
Avg. coverage 0.000 0.000 68.864 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 166
Avg. contig coverage: 68.864

Consensus contains: A: 919 C: 1946 G: 1885 T: 847 N: 0
IUPAC: 0 Funny: 0 *: 599
GC content: 68.447%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 45848
Localtime: Mon Jun 15 17:09:17 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 40985 cases.

P 1, marked 40985 reads.
Timing BFC edit tricky1: 28231
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 5 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 29549
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 240 positions.
Localtime: Mon Jun 15 17:09:17 2015
Deleting superfluous gap columns (2) ... done, deleted 99 columns.
Localtime: Mon Jun 15 17:09:17 2015
Timing BFC edit single discrepancy, no HAF: 28793
bfc 12/0
Timing BFC delPSHP: 295
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: 350
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 194
mict_pre 6
mict_shadow 64
mict_fallout 5523
mict_newin 3327
mict_helper1 19556
mict_newin 3327
mict_restofloop 3423
mict_totalloop 45062
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 106083
Contig coverage analysis ... Timing BFC loop total: 570135
bfc 1
Localtime: Mon Jun 15 17:09:17 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 33
Localtime: Mon Jun 15 17:09:17 2015
Unused reads: 1576505
bfc 8/0
0 Known 1: 2322
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 342
pft 13 / 121
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 657
pft 12 / 130
[121] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 730
pft 12 / 136
[180] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 778
pft 15 / 144
[239] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 877
pft 13 / 119
[298] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 914
pft 14 / 107
[358] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1134
pft 13 / 111
[418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1351
pft 13 / 115
[478] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1603
pft 14 / 111
[538] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1789
pft 11 / 126
[598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1971
pft 12 / 130
[658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2023
pft 15 / 122
[718] ++++++++++++++a+++++++++++++++++++++++a+++++++++++++++++++++ 2039
pft 23 / 107
[776] ++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 2045
pft 17 / 87
[835] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2055
pft 17 / 89
[894] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 2115
pft 13 / 130
[953] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2160
pft 16 / 159
[1013] +++++++++++++++++++++++++++++++++++++d++++++++++++++++++++++ 2167
pft 21 / 136
[1072] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2177
pft 23 / 130
[1132] +++++++++++++++++++++++++++++++++++++++++++a++++++GGG+++GG++ 2179
pft 22 / 93
[1186] ++++++GG++++++++++++++++++++++++++++++++++++++++++++++++++++ 2354
pft 13 / 106
[1244] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 2378
pft 11 / 121
[1303] ++++++++++++++++++++a+++++++++++++++++++++++d++++++a++++++++ 2381
pft 17 / 113
[1360] +++++++++++++aa++++aaa++a+++++++++++++aaaaa++++++d++aaaaaaapriv_ld
addRead: 176435
priv_ld total: 197336
Timing BFC paf construct: 197389

ccon timings:
cct pre 1008
cct dir 1481
cct xcu 6303
cct tmp 737
cct sw 108786
cct pic 768
cct ico 46214
cct icm 0
cct upd 856
cct del 0
cct rmz 808
cct gcp 147

ccon i timings (1398):
ccit insglcc 111
ccit insglaro 396
ccit insglact 49
ccit insgltot 1562
ccit pr 8481
ccit templ 1099
ccit index 755
ccit biglccins 1067
ccit biglinterpol 266
ccit biglupdtags 155
ccit biglfpcri 139
ccit bigllgap 6724
ccit biglshiftread 1451
ccit bigltot 19231
ccit insgr 767
ccit ucv 7455

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1399
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:17 2015
Timing BFC analysereadcov: 6180
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 43
mict_fallout 2633
mict_newin 1233
mict_helper1 11048
mict_newin 1233
mict_restofloop 1290
mict_totalloop 21381
done.

-------------- Contig statistics ----------------
Contig id: 33
Contig length: 2391

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1399 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 185 0 0
0 0 0
Avg. coverage 0.000 0.000 109.485 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 185
Avg. contig coverage: 109.485

Consensus contains: A: 343 C: 654 G: 712 T: 390 N: 0
IUPAC: 0 Funny: 0 *: 292
GC content: 65.079%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 21648
Localtime: Mon Jun 15 17:09:18 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 27618 cases.

P 1, marked 27618 reads.
Timing BFC edit tricky1: 18400
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 17392
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 441 cases.

Edited 441 reads.
Localtime: Mon Jun 15 17:09:18 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:18 2015
Timing BFC edit tricky2: 12678

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 98 positions.
Localtime: Mon Jun 15 17:09:18 2015
Deleting superfluous gap columns (2) ... done, deleted 162 columns.
Localtime: Mon Jun 15 17:09:18 2015
Timing BFC edit single discrepancy, no HAF: 25451
bfc 12/0
Timing BFC delPSHP: 174
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 7621
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 129
mict_pre 6
mict_shadow 42
mict_fallout 2437
mict_newin 1163
mict_helper1 10237
mict_newin 1163
mict_restofloop 1202
mict_totalloop 19901
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 55119
Timing BFC loop total: 362944
bfc 1
Localtime: Mon Jun 15 17:09:18 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 34
Localtime: Mon Jun 15 17:09:18 2015
Unused reads: 1575106
bfc 8/0
0 Known 1: 1399
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 426
pft 11 / 120
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 801
pft 10 / 114
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 977
pft 11 / 120
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1062
pft 12 / 124
[241] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 1147
pft 14 / 132
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1264
pft 15 / 122
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1589
pft 9 / 116
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1760
pft 11 / 116
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1875
pft 17 / 140
[540] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 2106
pft 12 / 120
[599] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 2138
pft 19 / 118
[658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2326
pft 20 / 111
[718] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 2456
pft 12 / 110
[777] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2488
pft 21 / 100
[837] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2503
pft 23 / 91
[897] +++++++++++a++++++++++++++++++++++++++++++++++++++++++++++++ 2515
pft 20 / 82
[956] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2562
pft 19 / 74
[1016] +++++++++++++++a+++++++++++++a++++++++++++++++++++++++++++++ 2895
pft 16 / 109
[1074] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2959
pft 11 / 119
[1134] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3083
pft 13 / 112
[1194] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3558
pft 12 / 114
[1254] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3652
pft 13 / 135
[1314] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3986
pft 13 / 132
[1374] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4166
pft 11 / 115
[1434] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4338
pft 12 / 118
[1494] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4404
pft 14 / 127
[1553] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4453
pft 18 / 135
[1613] ++++++++++++++++++++++++++++++++a+a++++a+++++++++a++++++++++ 4484
pft 18 / 122
[1669] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4496
pft 16 / 123
[1729] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 4541
pft 14 / 114
[1788] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4580
pft 13 / 121
[1848] ++++++++++++++++++a+++++++a+++++++++++++++++++++++++++++++++ 4586
pft 13 / 142
[1906] ++++++++++++++++++++a++d+++a++++++++aaa++++++++aaaaaaaaa+++a 4593
pft 11 / 133
[1949] aaaaa++++++aa+++aa+++a++d+a+++d+aa+a+++aaa+aa+aaa++++++++a++ 4600
pft 10 / 137
[1985] +++++++++++a+++aaa++aa+da+a+++a++++a+++++++++d+++ad+++++++++ 4631
pft 10 / 133
[2031] ++++++++++++++++a+++++++++a+d+++a++++++a++++++++a++a+d++++++ 4655
pft 11 / 141
[2083] +++++++++++++++++++++++++++++++++++a++++++++++++a+++++++++++ 5020
pft 12 / 134
[2141] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5217
pft 11 / 128
[2201] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5529
pft 10 / 119
[2261] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5734
pft 11 / 124
[2321] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5785
pft 14 / 134
[2381] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 5866
pft 16 / 129
[2440] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 5876
pft 17 / 113
[2499] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 6059
pft 13 / 115
[2558] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6322
pft 10 / 117
[2618] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6401
pft 13 / 141
[2678] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6466
pft 17 / 139
[2738] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 6674
pft 16 / 108
[2797] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6728
pft 11 / 117
[2857] +++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 6802
pft 17 / 117
[2916] ++++++++++++a+++++++++++++++++++++a++++++++a++++++++++++++++ 6817
pft 18 / 104
[2973] +++++++++++a++++++++++++++++++++++++++++++++++++++++++++++++ 6907
pft 13 / 109
[3032] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 7140
pft 12 / 122
[3091] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 7154
pft 14 / 119
[3150] +++++++++++++++++++++++++a+a++++++++++++++++++++++++a+++++++ 7168
pft 13 / 124
[3207] ++++++++++++++++++a++++++++a++++++++++++++++++++++++++++++++ 7505
pft 12 / 121
[3265] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7682
pft 12 / 120
[3325] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7945
pft 12 / 119
[3385] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7972
pft 19 / 145
[3445] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 8038
pft 20 / 95
[3504] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8258
pft 21 / 86
[3564] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8574
pft 9 / 122
[3624] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8688
pft 13 / 120
[3684] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 8893
pft 10 / 123
[3744] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9148
pft 13 / 124
[3804] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9192
pft 15 / 119
[3864] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9210
pft 17 / 128
[3924] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9275
pft 20 / 84
[3984] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9287
pft 17 / 77
[4044] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 9736
pft 12 / 113
[4104] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10019
pft 11 / 112
[4164] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10135
pft 14 / 137
[4224] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10149
pft 16 / 130
[4284] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10369
pft 17 / 119
[4344] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10417
pft 12 / 117
[4404] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 10479
pft 15 / 103
[4463] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++d+++ 10492
pft 17 / 150
[4521] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10858
pft 12 / 129
[4581] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 10963
pft 13 / 132
[4641] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11170
pft 10 / 121
[4701] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11301
pft 10 / 125
[4761] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11531
pft 10 / 121
[4821] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11809
pft 10 / 113
[4881] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11903
pft 16 / 144
[4941] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 11930
pft 13 / 130
[5000] +++++++++++++++++++++a+a+++++a++++++++++++++++++++++++++++++ 11965
pft 15 / 129
[5057] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 12027
pft 17 / 118
[5116] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12317
pft 10 / 123
[5176] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12456
pft 12 / 123
[5236] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12698
pft 12 / 120
[5296] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12751
pft 17 / 122
[5356] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12770
pft 17 / 128
[5416] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12820
pft 21 / 107
[5476] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12840
pft 19 / 102
[5536] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12867
pft 19 / 107
[5596] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 12886
pft 23 / 105
[5656] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a++a++ 12909
pft 17 / 99
[5714] +++++++++++++++++++++++++a++++++a+++a+++++++++++++++++++++++ 12955
pft 14 / 130
[5771] +++++++++++a+++++++++++++++++++++a+++++a++++++++++++++++++++ 13142
pft 13 / 140
[5828] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13438
pft 10 / 114
[5888] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13633
pft 13 / 111
[5948] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 13830
pft 11 / 114
[6008] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14029
pft 15 / 112
[6068] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 14095
pft 14 / 122
[6127] +++++++++++++++++++++++++++++++a+++++a++++++++++++++++++++++ 14159
pft 16 / 110
[6185] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14174
pft 15 / 107
[6245] +++a+++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 14641
pft 16 / 94
[6303] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14672
pft 12 / 136
[6363] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 14682
pft 14 / 170
[6422] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 14691
pft 12 / 130
[6481] +++++++++a++d+++++++++++++++++++++++++++++++++++++++++++++++ 14697
pft 13 / 153
[6539] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14700
pft 18 / 150
[6599] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14710
pft 24 / 163
[6659] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a 14728
pft 24 / 172
[6718] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 14737
pft 26 / 153
[6777] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14778
pft 26 / 139
[6836] +++a+++++++++++++++++++a++++++++++++++a+++++++++++++++a+++++ 14784
pft 20 / 141
[6892] +++++++++++++a++++++++++++++++a++++++++++++++++++a+++++a++++ 14799
pft 23 / 140
[6948] ++++++++++++++++++++++++++++++++a++++++++++++++a++a+++++++++ 14804
pft 24 / 135
[7005] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14810
pft 22 / 120
[7065] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 14817
pft 23 / 126
[7124] ++++++++++++++++++++++++++++++++++++++++a++++++++a+++a+aa+aa 14829
pft 20 / 138
[7177] +aaa+a+aa+a++++a++++GGGGGGGG+GGGGGGGGGGGGGGGGGGGGGGGGGGG+GGG 14830
pft 14 / 78
[7190] GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG+++aaaaaaa+a+GaGa++ 14831
pft 6 / 72
[7198] +++++GG++a+aaa+++aaaa++++++++++++++++++++++++++++++++++++aa+ 14837
pft 17 / 147
[7246] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14839
pft 19 / 160
[7306] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 14850
pft 17 / 168
[7366] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15249
pft 12 / 126
[7426] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 15597
pft 9 / 121
[7485] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15681
pft 15 / 131
[7545] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 15741
pft 17 / 146
[7605] +++++++++++++++++++++++++++++++++++++a+++++++++++++a++++++++ 15783
pft 15 / 128
[7663] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16025
pft 13 / 120
[7723] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16262
pft 10 / 117
[7783] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16376
pft 13 / 130
[7843] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16508
pft 17 / 120
[7903] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16741
pft 10 / 123
[7963] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16846
pft 13 / 136
[8023] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16872
pft 15 / 130
[8083] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16907
pft 17 / 115
[8143] +++++++++++++++++++a++++++++++++++++++++++++++++++++++++++++ 16923
pft 20 / 136
[8202] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 16930
pft 22 / 120
[8262] ++++++++++++++++++++a+++a+a+++++++++++++++++a++++++++++a++++ 17168
pft 13 / 110
[8317] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17528
pft 9 / 113
[8377] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17695
pft 11 / 122
[8437] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 17809
pft 11 / 136
[8497] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18093
pft 11 / 125
[8557] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 18145
pft 12 / 133
[8616] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18163
pft 17 / 124
[8676] ++++++++++++++++++++++a++a++++++++++++++++++++++++++++++++++ 18207
pft 19 / 112
[8734] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18256
pft 17 / 90
[8794] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++d+++ 18265
pft 20 / 86
[8852] ++++a+++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 18372
pft 11 / 132
[8910] +++++++++++++++++++++++++++a++++++++++++++++++++++++++++++++ 18386
pft 16 / 164
[8969] +++++a+++++++++++++++++++++++++++++++++a+++++++++++++++a++++ 18401
pft 26 / 159
[9026] ++a++++++++++++++++++++++++++++++++++++++++++++++++++a++++++ 18408
pft 17 / 111
[9084] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 18413
pft 25 / 163
[9144] +++++++++++++++++++++++++++++++++++++++++++++++++aa+++++++++ 18417
pft 15 / 158
[9202] ++++++++++++++++++++a+++++++++++++++++a++++++++++a+++++++++a 18423
pft 27 / 160
[9258] +++++++++a++++++++++++++++++++++++++a++++++++++++++a++++a+++ 18432
pft 38 / 163
[9314] ++++++++a++a+++++++++++++a++++++++++++++d++++d++++++++++++++ 18440
pft 38 / 142
[9368] a+a+++++a+++++++a++++++++++++a++++++++++++++++++a+++++++++++ 18447
pft 36 / 121
[9423] ++++++++++++++a++++aa+++++++++d++++++++aa+++++++++++++++++++ 18452
pft 29 / 89
[9477] +++++++aaaaaaaaaaaaaaaa+++++a++++++a+a+++++++++++aa++a++++a+ 18453
pft 13 / 146
[9514] +aaa++++++a++a+++a+++++a++++a++++aa+a+++a++aaaa+++++a+a++aaa 18461
pft 29 / 178
[9552] a+a+++++a++++a++++a+a+++a+aaa+a+aaa+++++++++++++++++++++++++ 18465
pft 21 / 145
[9599] ++++++++++++++++++++++++++++++++++++++++++a+++++a+++++++++++ 18474
pft 23 / 146
[9657] ++++a++++++++++++a+++++++++a+++++a+++++++++++++a+a++++++++a+ 18484
pft 34 / 133
[9710] ++++++++a++++++++a+++a++++++++++++aa+a++a+++++a+a++++a++++++ 18489
pft 22 / 94
[9760] ++++++++++++++++aa++GG++++G++G+GGa++a+a++a++aaG+++GG+++GGa++ 18494
pft 14 / 132
[9800] +++++G+G++G++++aGG+a+a+GG+GGaGG+++++GG++Ga+++G+aa+G++++GGGGG 18501
pft 19 / 125
[9832] +a+aG++GGa+a+++++++G+++++GGGG+GG+GGGGGG+GG++++++++++++++++++ 18736
pft 12 / 113
[9870] +++++++a++++++++a++a++++a++a++++++++++++++++++++++++++++++++ 18973
pft 9 / 113
[9925] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19119
pft 13 / 102
[9985] ++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++aa 19125
pft 16 / 116
[10041] aa++++++++++++++++++++++a+++++++++++++++++++++aaa+++++++++++ 19169
pft 25 / 151
[10096] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 19469
pft 11 / 125
[10155] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19620
pft 10 / 126
[10215] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 19789
pft 10 / 115
[10275] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20040
pft 11 / 124
[10335] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20058
pft 12 / 126
[10395] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20107
pft 15 / 128
[10455] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20154
pft 15 / 118
[10515] ++a+++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 20204
pft 15 / 108
[10573] ++++++++++++++++d+d++++++++a++++++++++++++++++++++++++++++++ 20366
pft 13 / 124
[10630] +++++++++++++++++++++++++++++++++d++++++++++++++++d+++++++++ 20379
pft 11 / 141
[10688] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20484
pft 13 / 147
[10748] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20665
pft 12 / 127
[10808] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++a+ 20670
pft 9 / 117
[10866] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 20688
pft 10 / 136
[10924] a++++a+++++a+++++++++a+++++++a++a+++++++++++++++++++a+a+++++ 20696
pft 18 / 130
[10977] +++++++++++++++++++++++++++aa+++++++++++++++++++++++++++++++ 20701
pft 17 / 144
[11035] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 20709
pft 21 / 159
[11095] +++++++++++++++++a+++++++++++++++++++++++++aa+++++++++++++++ 20722
pft 41 / 142
[11152] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 20722
pft 16 / 150
[11211] +++++++++++++aa+++++++++++++++++d++++++++++++++++da+++++a+++ 20725
pft 17 / 155
[11265] +++++++++a++++++++++++a++++++++++++a++++++++++++a++a+a++++++ 20731
pft 29 / 141
[11319] ++a++++++++++a++++++a++a++++++++++++++++++aaaa+aa+a+++++++++ 20742
pft 28 / 144
[11368] +++++++a++++++++++++++++++++++++++++++++++++++a++a++++++++aa 20747
pft 29 / 135
[11423] +++++++++++++++++++++++++++++++++++++aaa+aa++a+++a+++a++a++a 20752
pft 48 / 116
[11472] aaaa++a++a+++++++++aa+++++++a+a+a+a+++a++a++++++++++++aa++++ 20754
pft 47 / 102
[11517] ++++++a+++++++aa+a+a+++++aa+++a+a+++a+aa++++a+++++++++++++++ 20757
pft 52 / 95
[11564] +a++a++++++aaaaa++aaaaaaaaaaaaaaaaaa+++aaa++++++aa+++++aaa++ 20758
pft 36 / 107
[11591] +a+a++++++++++++++a++++++a++++aaaaaaaaaa+aaaaa+aaaaaaaaa+aaa 20759
pft 384 / 96
[11619] a+++aa+aa+a++++++aaa++d+++ad+aa+a+++++++a+a+aa+a+++a++++a+aa 20765
pft 15 / 150
[11656] +aaa+a+adaaa+++aaa+aa+++++++++++a+a++++aa+++++a++a+aa+++a+aa 20768
pft 39 / 149
[11691] +aa+aaaa+a+++a+a+a+aaaaa+aaaaaaa+++a+++++++++aa++aaa+a+aaaaa 20771
pft 72 / 148
[11716] aaaaaaaaa+a+aaaa+aaaaa+aaaaaaa+aaaaaaaa+aaaaa++++a++++++++++ 20773
pft 19 / 135
[11737] ++++++++++++++++a+a++++++++++a++++a+a++aa++a++++aaa+aaaaa+aa 20776
pft 75 / 160
[11778] a+aaaaaaaa+aaaaaaaaaaaa+aaaaaaa+aaaaaaaaaaaaa++a++++++++++++ 20778
pft 30 / 144
[11797] ++++++aa+++++aaa+a+aaaa++a+++aaa++a+aaa+aa+aaaaaaaaaaa+aaa+a 20783
pft 96 / 158
[11821] aaaa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaaaaa+aaaaaaaaa 20784
pft 158 / 131
[11825] +aadaaaaaa+aaaaaaaaaaaaadaaaaaaaa+aaaaaaaaaaaaaaaaaaaaaaaaaa 20784
pft 4 / 119
[11827] aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaapriv_ld addRead: 1640198
priv_ld total: 1868455
Timing BFC paf construct: 1868506

ccon timings:
cct pre 9473
cct dir 18352
cct xcu 59758
cct tmp 6762
cct sw 1012427
cct pic 6586
cct ico 426337
cct icm 0
cct upd 7485
cct del 0
cct rmz 7215
cct gcp 4817

ccon i timings (11826):
ccit insglcc 372
ccit insglaro 1222
ccit insglact 159
ccit insgltot 9145
ccit pr 75844
ccit templ 12463
ccit index 6281
ccit biglccins 18877
ccit biglinterpol 2347
ccit biglupdtags 1399
ccit biglfpcri 1351
ccit bigllgap 75864
ccit biglshiftread 10935
ccit bigltot 193092
ccit insgr 6978
ccit ucv 64906

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 11827
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:20 2015
Timing BFC analysereadcov: 56128
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 10
mict_shadow 458
mict_fallout 23400
mict_newin 11505
mict_helper1 98937
mict_newin 11505
mict_restofloop 11539
mict_totalloop 190091
done.

-------------- Contig statistics ----------------
Contig id: 34
Contig length: 20784

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 11827 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 291 0 0
0 0 0
Avg. coverage 0.000 0.000 109.726 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 291
Avg. contig coverage: 109.726

Consensus contains: A: 3224 C: 6073 G: 5870 T: 3155 N: 0
IUPAC: 0 Funny: 0 *: 2462
GC content: 65.184%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 193563
Localtime: Mon Jun 15 17:09:20 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 241002 cases.

P 1, marked 241002 reads.
Timing BFC edit tricky1: 157976
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 104 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 188291
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 1080 positions.
Localtime: Mon Jun 15 17:09:20 2015
Deleting superfluous gap columns (2) ... done, deleted 301 columns.
Localtime: Mon Jun 15 17:09:20 2015
Timing BFC edit single discrepancy, no HAF: 166242
bfc 12/0
Timing BFC delPSHP: 3240
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: 5066
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 1367
mict_pre 7
mict_shadow 461
mict_fallout 22929
mict_newin 11291
mict_helper1 97415
mict_newin 11291
mict_restofloop 11141
mict_totalloop 187123
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 553199
Contig coverage analysis ... Timing BFC loop total: 3203800
bfc 1
Localtime: Mon Jun 15 17:09:21 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 2
bfc 5
bfc 6/0
bfc 7/0
Building new contig 35
Localtime: Mon Jun 15 17:09:21 2015
Unused reads: 1563279
bfc 8/0
0 Known 1: 11827
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 592
pft 11 / 112
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 804
pft 11 / 111
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 880
pft 11 / 133
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 967
pft 15 / 138
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1400
pft 10 / 110
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1438
pft 17 / 123
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1773
pft 11 / 110
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2018
pft 10 / 126
[481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2250
pft 10 / 119
[541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2381
pft 11 / 122
[601] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2473
pft 20 / 154
[661] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2648
pft 18 / 121
[721] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2786
pft 12 / 123
[781] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2807
pft 20 / 113
[841] ++++++++++++++++++++a+++++++++++++++++++a+++++++++++++++++++ 2857
pft 22 / 107
[899] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 2869
pft 21 / 98
[958] +++++++++++++++++++++++++++++++++++++++++++++a++a+++++++++++ 2888
pft 21 / 91
[1016] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3242
pft 13 / 116
[1076] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3422
pft 11 / 126
[1136] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3444
pft 14 / 126
[1196] ++++++++++++++++++++++++++a+a++++++++++++++++++++++a++++++++ 3451
pft 17 / 99
[1253] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3468
pft 22 / 81
[1313] ++++++++++++a+++++++++++++++++++a+++++++++++++++++++++++++++ 3484
pft 22 / 80
[1371] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 3804
pft 18 / 112
[1430] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4005
pft 11 / 129
[1490] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4165
pft 11 / 124
[1550] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4188
pft 16 / 134
[1610] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4199
pft 17 / 120
[1670] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4212
pft 19 / 99
[1730] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 4258
pft 15 / 102
[1789] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4656
pft 11 / 121
[1849] +++++++++++++++++++++++a++++++a+a+a+++++++++a++++++a+++aa+++ 4737
pft 12 / 107
[1901] +++++++++++++++++++aa++++++++++++++++a++++++++++++++++++++++ 4834
pft 11 / 132
[1958] ++++++++++++++++++++++a++++++++++++++++++++++++++++++++++a++ 4840
pft 16 / 154
[2016] +a+++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 4852
pft 22 / 127
[2074] ++++++++++++++++++++++++++++++a++++++++++++++++++++++G+++++G 4860
pft 23 / 145
[2130] G+G+++++++++GG++++++++++++++++++G+++++++++++++++++++++++++++ 4992
pft 15 / 132
[2186] ++++++++++++++++++++++++++++++++++++a++++G+++GG++G+++G++G+++ 5003
pft 22 / 120
[2238] G+++G++G++G+G++GGG++GGGGG+++++GGG++++GGGGG+GG++G+++++GGGG++G 5007
pft 10 / 112
[2269] GG++G+GGG+G+G+G+++GGGGG++G++GG+GGG+GG++G++G+GGGG+++G+GG+G+G+ 5009
pft 16 / 82
[2297] +++G+GGGGGGGGGGGGGGG+G+G++++GGGGG+G+G+GGG+GG++++GG++Gaaaaaaa 5009
pft 74 / 68
[2316] aaaaaaaa+++++G+aGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG+GGG 5010
pft 9 / 105
[2323] GGGGGGGGGGGGGGaGGGGGGGGGGG+GGGGGGaGGGGGGGGGGGGGGGGGGGGGGGGGG 5010
pft 45 / 81
[2324] GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 305690
priv_ld total: 346779
Timing BFC paf construct: 346887

ccon timings:
cct pre 1883
cct dir 3454
cct xcu 8858
cct tmp 1404
cct sw 190710
cct pic 1227
cct ico 78045
cct icm 0
cct upd 1435
cct del 0
cct rmz 1409
cct gcp 807

ccon i timings (2323):
ccit insglcc 53
ccit insglaro 161
ccit insglact 18
ccit insgltot 1666
ccit pr 14307
ccit templ 1954
ccit index 1277
ccit biglccins 2560
ccit biglinterpol 547
ccit biglupdtags 325
ccit biglfpcri 280
ccit bigllgap 12833
ccit biglshiftread 2330
ccit bigltot 33901
ccit insgr 1397
ccit ucv 12236

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2324
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:21 2015
Timing BFC analysereadcov: 10786
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 66
mict_fallout 5012
mict_newin 2780
mict_helper1 19684
mict_newin 2780
mict_restofloop 2714
mict_totalloop 41117
done.

-------------- Contig statistics ----------------
Contig id: 35
Contig length: 5010

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2324 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 182 0 0
0 0 0
Avg. coverage 0.000 0.000 86.804 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 182
Avg. contig coverage: 86.804

Consensus contains: A: 703 C: 1450 G: 1520 T: 762 N: 0
IUPAC: 0 Funny: 0 *: 575
GC content: 66.967%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 41701
Localtime: Mon Jun 15 17:09:21 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 46574 cases.

P 1, marked 46574 reads.
Timing BFC edit tricky1: 28604
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 29989
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 927 cases.

Edited 927 reads.
Localtime: Mon Jun 15 17:09:21 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:21 2015
Timing BFC edit tricky2: 20873

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 230 positions.
Localtime: Mon Jun 15 17:09:21 2015
Deleting superfluous gap columns (2) ... done, deleted 344 columns.
Localtime: Mon Jun 15 17:09:21 2015
Timing BFC edit single discrepancy, no HAF: 47167
bfc 12/0
Timing BFC delPSHP: 377
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 12640
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 314
mict_pre 6
mict_shadow 67
mict_fallout 4500
mict_newin 2471
mict_helper1 17234
mict_newin 2471
mict_restofloop 2547
mict_totalloop 36787
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 95757
Timing BFC loop total: 636342
bfc 1
Localtime: Mon Jun 15 17:09:22 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 36
Localtime: Mon Jun 15 17:09:22 2015
Unused reads: 1560955
bfc 8/0
0 Known 1: 2324
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 456
pft 11 / 117
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 550
pft 15 / 126
[121] +++++++++++++++++++++++++++++++a+++a++++++++++++++++++++++++ 720
pft 16 / 110
[179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 908
pft 10 / 114
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1051
pft 13 / 119
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1266
pft 12 / 125
[359] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1347
pft 18 / 146
[419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1405
pft 17 / 138
[479] +++++++++++++++++++++++d++++++++++++++++++++++++++++++++++++ 1436
pft 18 / 124
[538] ++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++a 1483
pft 17 / 110
[596] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1495
pft 16 / 112
[656] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1790
pft 13 / 109
[716] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1879
pft 13 / 122
[776] ++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++ 1915
pft 12 / 123
[835] ++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++ 1960
pft 16 / 109
[894] ++++++++++++++++++++++++++++++++++++++++a++++++++++++a++++++ 2137
pft 10 / 119
[952] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2376
pft 11 / 107
[1012] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2701
pft 11 / 114
[1072] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2908
pft 16 / 131
[1132] ++++++++++a+++++++a++++++++++a++++++++++++++++++++++++++++++ 2952
pft 17 / 111
[1189] +++++++++++a++++++++++++++++++a+++++++++++++++++a+++++++a+++ 2990
pft 14 / 122
[1245] ++++a++a++++++++++a+++++++++a++a++++a++a++++a+++++++++++++a+ 3001
pft 15 / 95
[1296] +a++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 3280
pft 12 / 117
[1354] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++ 3343
pft 13 / 126
[1413] +++++++++++++++++++++++++++++++++a+++++++++++++a+a+++++++a++ 3415
pft 14 / 109
[1469] +++++++++++++++++++++++++++++++++++++a++++++++++aa++++++++++ 3451
pft 15 / 104
[1526] ++a+a+++++++++++++++++d+++++++++++++++++++++++++++++a+++++++ 3620
pft 13 / 136
[1582] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3650
pft 9 / 131
[1642] ++++++++++a++++++++++++++++++a+a++++++++++++++++++++++++++++ 3901
pft 11 / 117
[1699] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4041
pft 12 / 111
[1759] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4223
pft 17 / 133
[1819] +++++++a++++++++++++++++++++++++++++++++++++++a+++++++++++++ 4232
pft 12 / 164
[1877] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4236
pft 18 / 159
[1937] +++++++++++++++++++++++a++++++++++++++a+++++++++++++++++++++ 4242
pft 26 / 146
[1995] ++++++++++++++++++++a++++++++++++++++++++++a++++++++++++++++ 4253
pft 29 / 139
[2053] +++++++++++++a++++++++++++++++++++++++++++++++++++++++++++++ 4307
pft 18 / 111
[2112] ++++++++++++++++++++++++++++++++++++++++++++++aa+++a++++++++ 4685
pft 10 / 117
[2169] +++a+++++++++++++++++++++++a+++++++++++a++++++++++++++a+++++ 4766
pft 11 / 121
[2225] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5064
pft 12 / 123
[2285] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 5133
pft 12 / 113
[2344] ++++++++++++++++++++++++++++++++++a++++++++++a++++++++++++++ 5253
pft 13 / 108
[2402] +++++++++++++++++++++++++++++++++++++++++++++a+++a++++a+++++ 5286
pft 14 / 97
[2459] ++a+++++++++++++++++++++++a++++++++++++++++++++++++aaa+++++a 5311
pft 14 / 159
[2513] +++++++++a++++++++++++++++++++++++++++++++++++++++++++++++++ 5321
pft 17 / 137
[2572] +++++++++++++++++++++++++++++++a++++++++++++++++++++++++++++ 5327
pft 18 / 144
[2631] ++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++ 5332
pft 17 / 159
[2690] +++++++++++++++++++++++++++++a++++++++++++++++a+++++++++++++ 5338
pft 28 / 146
[2748] +++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++a 5346
pft 23 / 139
[2806] +++++++++++++++++++++++++++++++++++++++++++++++a++++++++++++ 5350
pft 16 / 157
[2865] +++++++++++++++++++++++++++++++++++++++++++++++a+++++a++++++ 5358
pft 27 / 138
[2923] +++a++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 5366
pft 36 / 92
[2981] +++++++++++++++d+++++aaaa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+aaa 5368
pft 66 / 95
[3002] aaaaaaaaaaaaaaaaaaaaadpriv_ld addRead: 398221
priv_ld total: 444683
Timing BFC paf construct: 444745

ccon timings:
cct pre 2310
cct dir 3489
cct xcu 15166
cct tmp 1630
cct sw 245575
cct pic 1589
cct ico 104104
cct icm 0
cct upd 1882
cct del 0
cct rmz 1812
cct gcp 463

ccon i timings (3001):
ccit insglcc 220
ccit insglaro 714
ccit insglact 92
ccit insgltot 3084
ccit pr 18936
ccit templ 2658
ccit index 1610
ccit biglccins 3206
ccit biglinterpol 596
ccit biglupdtags 342
ccit biglfpcri 329
ccit bigllgap 17130
ccit biglshiftread 3230
ccit bigltot 45100
ccit insgr 1676
ccit ucv 16427

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3002
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:22 2015
Timing BFC analysereadcov: 15016
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 99
mict_fallout 5833
mict_newin 2862
mict_helper1 24456
mict_newin 2862
mict_restofloop 2920
mict_totalloop 47624
done.

-------------- Contig statistics ----------------
Contig id: 36
Contig length: 5368

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3002 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 230 0 0
0 0 0
Avg. coverage 0.000 0.000 108.010 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 230
Avg. contig coverage: 108.010

Consensus contains: A: 704 C: 1426 G: 1667 T: 936 N: 0
IUPAC: 0 Funny: 0 *: 635
GC content: 65.350%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 48251
Localtime: Mon Jun 15 17:09:22 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 60469 cases.

P 1, marked 60469 reads.
Timing BFC edit tricky1: 36621
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 42398
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 998 cases.

Edited 998 reads.
Localtime: Mon Jun 15 17:09:22 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:22 2015
Timing BFC edit tricky2: 26574

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 288 positions.
Localtime: Mon Jun 15 17:09:22 2015
Deleting superfluous gap columns (2) ... done, deleted 381 columns.
Localtime: Mon Jun 15 17:09:22 2015
Timing BFC edit single discrepancy, no HAF: 61608
bfc 12/0
Timing BFC delPSHP: 614
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 17070
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 343
mict_pre 6
mict_shadow 91
mict_fallout 5438
mict_newin 2684
mict_helper1 22563
mict_newin 2684
mict_restofloop 2737
mict_totalloop 44041
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 122336
Timing BFC loop total: 818266
bfc 1
Localtime: Mon Jun 15 17:09:22 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 37
Localtime: Mon Jun 15 17:09:22 2015
Unused reads: 1557953
bfc 8/0
0 Known 1: 3002
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 477
pft 12 / 117
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 560
pft 14 / 120
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 628
pft 15 / 120
[179] a+++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 892
pft 11 / 131
[238] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 939
pft 15 / 160
[298] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 994
pft 13 / 126
[357] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1331
pft 11 / 113
[417] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 1471
pft 12 / 128
[476] +++++++++++a+++++++++++++++++++++++++a+++++++a++++++++++++++ 1586
pft 13 / 135
[533] +++a++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1906
pft 11 / 117
[592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2125
pft 10 / 115
[652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2376
pft 10 / 112
[712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2395
pft 14 / 127
[772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2474
pft 14 / 125
[832] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 2526
pft 17 / 120
[891] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 2547
pft 19 / 122
[950] +++++++++a++++++++++++++++++++++++++++++++++++++++a++a++++++ 2569
pft 20 / 127
[1007] ++++++++++++a++++++a++++++++++++++++++++++++++++++++++++++++ 2610
pft 17 / 111
[1065] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 2631
pft 18 / 104
[1124] +++++++++++++++++++++++++++++++++++++++++++++++aaa++++++++++ 2654
pft 18 / 98
[1181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3177
pft 12 / 127
[1241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3360
pft 12 / 126
[1301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3410
pft 12 / 132
[1361] ++++++++++++++++a++++++++++++++++++++++++++++++++++++++a++++ 3423
pft 15 / 119
[1419] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3436
pft 16 / 101
[1479] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3442
pft 14 / 96
[1539] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 3461
pft 15 / 107
[1598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 3471
pft 10 / 134
[1657] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3877
pft 12 / 110
[1717] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 4111
pft 16 / 138
[1776] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4293
pft 12 / 118
[1836] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4360
pft 15 / 130
[1896] ++++++++++++++++++++++++++++++++++++++a++a++++++++++++++++++ 4378
pft 15 / 119
[1954] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4387
pft 17 / 100
[2014] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4397
pft 17 / 91
[2074] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4414
pft 19 / 141
[2134] +++++++++++da++++++++++++++++++++++++++++++++++++++++++a++++ 4424
pft 10 / 148
[2191] +++++++a+++++++++++++++++++++++++++++++++++++++++++++++++a++ 4429
pft 17 / 156
[2249] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 4436
pft 29 / 145
[2308] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++ 4442
pft 23 / 117
[2367] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4446
pft 25 / 109
[2427] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4449
pft 29 / 152
[2487] +++++++++++++++++++a++++a+++++++++++++++++++++++++++++++++++ 4457
pft 28 / 128
[2545] +++++++++++++++++++a+++++aaaaaaaaaaa+aaaaaaaaaaaaa+daapriv_ld addRead:
328511
priv_ld total: 366685
Timing BFC paf construct: 366748

ccon timings:
cct pre 1865
cct dir 3275
cct xcu 11550
cct tmp 1372
cct sw 201328
cct pic 1436
cct ico 87221
cct icm 0
cct upd 1681
cct del 0
cct rmz 1559
cct gcp 254

ccon i timings (2569):
ccit insglcc 74
ccit insglaro 255
ccit insglact 25
ccit insgltot 1964
ccit pr 15938
ccit templ 2254
ccit index 1399
ccit biglccins 2820
ccit biglinterpol 495
ccit biglupdtags 305
ccit biglfpcri 292
ccit bigllgap 14166
ccit biglshiftread 2404
ccit bigltot 37810
ccit insgr 1537
ccit ucv 13882

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2570
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:23 2015
Timing BFC analysereadcov: 11637
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 76
mict_fallout 4873
mict_newin 2398
mict_helper1 20585
mict_newin 2398
mict_restofloop 2473
mict_totalloop 39707
done.

-------------- Contig statistics ----------------
Contig id: 37
Contig length: 4459

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2570 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 202 0 0
0 0 0
Avg. coverage 0.000 0.000 109.170 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 202
Avg. contig coverage: 109.170

Consensus contains: A: 611 C: 1252 G: 1300 T: 756 N: 0
IUPAC: 0 Funny: 0 *: 540
GC content: 65.119%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 40146
Localtime: Mon Jun 15 17:09:23 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 49845 cases.

P 1, marked 49845 reads.
Timing BFC edit tricky1: 32879
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 33182
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 854 cases.

Edited 854 reads.
Localtime: Mon Jun 15 17:09:23 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:23 2015
Timing BFC edit tricky2: 22315

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 203 positions.
Localtime: Mon Jun 15 17:09:23 2015
Deleting superfluous gap columns (2) ... done, deleted 296 columns.
Localtime: Mon Jun 15 17:09:23 2015
Timing BFC edit single discrepancy, no HAF: 50310
bfc 12/0
Timing BFC delPSHP: 485
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 14866
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 296
mict_pre 6
mict_shadow 79
mict_fallout 4544
mict_newin 2229
mict_helper1 18971
mict_newin 2229
mict_restofloop 2262
mict_totalloop 36904
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 103720
Timing BFC loop total: 677872
bfc 1
Localtime: Mon Jun 15 17:09:23 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 38
Localtime: Mon Jun 15 17:09:23 2015
Unused reads: 1555383
bfc 8/0
0 Known 1: 2570
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 514
pft 11 / 115
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 720
pft 11 / 128
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 821
pft 14 / 130
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 979
pft 16 / 126
[241] +++++++++++++++++++++++++++++a++++++++++++++++++++a++++++a++ 1084
pft 12 / 116
[298] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 1214
pft 12 / 131
[357] +++++++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 1343
pft 15 / 114
[416] +a++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 1384
pft 18 / 131
[474] +++a++++++++++++++++++++++++++++++++++++++a+++++++++++++++++ 1485
pft 15 / 95
[532] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1989
pft 10 / 107
[592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2233
pft 9 / 121
[652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2501
pft 9 / 119
[712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2526
pft 11 / 135
[772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2778
pft 11 / 126
[832] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 2846
pft 17 / 121
[891] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3001
pft 10 / 118
[951] +++++++++++++++++++++++++++++++++++++++++++++++++++a++++++++ 3010
pft 18 / 101
[1010] ++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++ 3018
pft 19 / 86
[1069] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3234
pft 20 / 80
[1129] +++++++++++++++++++++++++++++a+++++++a++++++++++a+++++++++++ 3318
pft 13 / 122
[1186] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3652
pft 12 / 130
[1246] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3766
pft 9 / 129
[1306] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3909
pft 12 / 128
[1366] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3920
pft 15 / 109
[1426] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4272
pft 13 / 105
[1486] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4340
pft 14 / 120
[1546] ++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++++ 4432
pft 15 / 115
[1605] ++++++++++++++++++++++++++++a++++++++++++a+++++++++++++++a++ 4605
pft 14 / 126
[1662] +++++++++++++++++++++++++++++++++a++++++++++++++++++++++++++ 4641
pft 11 / 139
[1721] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4646
pft 17 / 153
[1781] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4658
pft 28 / 152
[1841] ++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++++ 4665
pft 28 / 105
[1900] ++aa++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4666
pft 40 / 126
[1958] +++++++++++++++++a++++++++++++++++++++++++++++++++++++++++++ 4679
pft 24 / 145
[2017] +++++++++++++++++++++++++++++++++++++++++++++++++++aGGa+++++ 4689
pft 27 / 123
[2073] ++++++++++++aa+a++++++++++++++++++++++++++++++++++++++++++++ 5126
pft 15 / 118
[2130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5156
pft 14 / 120
[2190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5520
pft 10 / 120
[2250] +++++++++++++++++++++++++++++++++++++a+++++++++++++++a++++++ 5553
pft 13 / 112
[2308] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5578
pft 16 / 98
[2368] ++++++++a+++++++++++++++++++++++++++++++++++++++++++++++a+++ 6038
pft 10 / 115
[2426] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6505
pft 10 / 100
[2486] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6731
pft 11 / 116
[2546] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6784
pft 16 / 123
[2606] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6795
pft 15 / 131
[2666] +++++++a++++++++++++++a+++++++++++++++++++++++++++++++++++++ 6805
pft 17 / 150
[2724] +++++++++++++++++++++++++++++a++++a+aaaa++++++GGG+G+++++++++ 6812
pft 22 / 143
[2774] ++++++++++++++G++++++++++++++++G++G++++G++++++++++++++++++++ 6817
pft 14 / 149
[2830] +++++++++++G++++++GGG+++G+++++++++GG+++++G++++++aa+GG+++++G+ 6821
pft 17 / 139
[2877] ++G+++++++G++GG+++GG+G+GG+G++++G++G++G+++++++G+++++++++GGG+G 6829
pft 22 / 125
[2918] GGGGG+GG+GGGG+G++G+++G+GGGG++++++GG+GGGGG++G++++++GaGG++++++ 6832
pft 20 / 88
[2949] +G+GGGGGGGGGGGGG+++++GGGGGGGGGGGGGGGGGGG+++GGG+GGGG+GGGG+++G 6833
pft 16 / 58
[2964] +GG++GG++++++G+++++++++aaaaaaaaaaaaaaaaaaaaaaaaaa++aaGGG+GGG 6833
pft 79 / 91
[2984] GGGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGGGGGGGGGGGGa+GGGGaaGGGGGGG 6833
pft 38 / 85
[2985] GGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead: 394534
priv_ld total: 444035
Timing BFC paf construct: 444092

ccon timings:
cct pre 2323
cct dir 3736
cct xcu 12466
cct tmp 1805
cct sw 246061
cct pic 1631
cct ico 101388
cct icm 0
cct upd 1833
cct del 0
cct rmz 1817
cct gcp 770

ccon i timings (2984):
ccit insglcc 346
ccit insglaro 1112
ccit insglact 135
ccit insgltot 3929
ccit pr 18930
ccit templ 2656
ccit index 1581
ccit biglccins 3358
ccit biglinterpol 618
ccit biglupdtags 355
ccit biglfpcri 333
ccit bigllgap 14719
ccit biglshiftread 3361
ccit bigltot 41883
ccit insgr 1673
ccit ucv 16174

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2985
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:23 2015
Timing BFC analysereadcov: 13872
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 6
mict_shadow 89
mict_fallout 6676
mict_newin 3748
mict_helper1 25661
mict_newin 3748
mict_restofloop 3838
mict_totalloop 54849
done.

-------------- Contig statistics ----------------
Contig id: 38
Contig length: 6833

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2985 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 237 0 0
0 0 0
Avg. coverage 0.000 0.000 83.515 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 237
Avg. contig coverage: 83.515

Consensus contains: A: 1102 C: 2038 G: 2090 T: 927 N: 0
IUPAC: 0 Funny: 0 *: 676
GC content: 67.046%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 55659
Localtime: Mon Jun 15 17:09:24 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 57930 cases.

P 1, marked 57930 reads.
Timing BFC edit tricky1: 36236
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 40327
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1075 cases.

Edited 1075 reads.
Localtime: Mon Jun 15 17:09:24 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:24 2015
Timing BFC edit tricky2: 26771

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 246 positions.
Localtime: Mon Jun 15 17:09:24 2015
Deleting superfluous gap columns (2) ... done, deleted 426 columns.
Localtime: Mon Jun 15 17:09:24 2015
Timing BFC edit single discrepancy, no HAF: 62932
bfc 12/0
Timing BFC delPSHP: 621
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 16258
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 451
mict_pre 5
mict_shadow 88
mict_fallout 6067
mict_newin 3415
mict_helper1 23119
mict_newin 3415
mict_restofloop 3391
mict_totalloop 49857
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 125274
Contig coverage analysis ... Timing BFC loop total: 825258
bfc 1
Localtime: Mon Jun 15 17:09:24 2015

bfc 2
Timing BFC prelim1: 3
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 39
Localtime: Mon Jun 15 17:09:24 2015
Unused reads: 1552398
bfc 8/0
0 Known 1: 2985
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] +++++++++++++++++++++++++++++++++++++++++++++++a++++++++++a+ 443
pft 11 / 114
[59] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 558
pft 11 / 114
[119] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 662
pft 10 / 109
[179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1010
pft 10 / 117
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1276
pft 11 / 115
[299] ++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++ 1411
pft 17 / 138
[358] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1476
pft 13 / 123
[418] ++++++++++++++a+++++++++++++++++++++++++++++++++++++++++++++ 1517
pft 14 / 115
[477] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1748
pft 15 / 105
[537] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 1823
pft 11 / 117
[596] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 2084
pft 12 / 110
[655] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2094
pft 9 / 132
[715] ++++++++++++++aa++++++a+++++++++++++++++++++++++++++++++++++ 2097
pft 12 / 141
[772] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 2107
pft 15 / 158
[831] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 2115
pft 24 / 145
[890] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 2123
pft 31 / 113
[949] +++++++++++++++++++++++++++++++++++++++++++++++++++++++aaaaa 2125
pft 29 / 72
[1004] +a+apriv_ld addRead: 125483
priv_ld total: 139037
Timing BFC paf construct: 139101

ccon timings:
cct pre 715
cct dir 950
cct xcu 5105
cct tmp 527
cct sw 77710
cct pic 551
cct ico 32039
cct icm 0
cct upd 649
cct del 0
cct rmz 640
cct gcp 55

ccon i timings (1004):
ccit insglcc 12
ccit insglaro 42
ccit insglact 6
ccit insgltot 648
ccit pr 6021
ccit templ 782
ccit index 549
ccit biglccins 802
ccit biglinterpol 196
ccit biglupdtags 106
ccit biglfpcri 102
ccit bigllgap 4295
ccit biglshiftread 843
ccit bigltot 13163
ccit insgr 604
ccit ucv 5348

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1005
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:24 2015
Timing BFC analysereadcov: 5510
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 33
mict_fallout 2118
mict_newin 1153
mict_helper1 8243
mict_newin 1153
mict_restofloop 1128
mict_totalloop 17200
done.

-------------- Contig statistics ----------------
Contig id: 39
Contig length: 2125

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 1005 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 168 0 0
0 0 0
Avg. coverage 0.000 0.000 88.357 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 168
Avg. contig coverage: 88.357

Consensus contains: A: 314 C: 617 G: 627 T: 357 N: 0
IUPAC: 0 Funny: 0 *: 210
GC content: 64.961%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 17468
Localtime: Mon Jun 15 17:09:24 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 18493 cases.

P 1, marked 18493 reads.
Timing BFC edit tricky1: 11828
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 13069
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 329 cases.

Edited 329 reads.
Localtime: Mon Jun 15 17:09:24 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:24 2015
Timing BFC edit tricky2: 9658

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 117 positions.
Localtime: Mon Jun 15 17:09:24 2015
Deleting superfluous gap columns (2) ... done, deleted 112 columns.
Localtime: Mon Jun 15 17:09:24 2015
Timing BFC edit single discrepancy, no HAF: 18133
bfc 12/0
Timing BFC delPSHP: 122
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 5353
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 85
mict_pre 5
mict_shadow 31
mict_fallout 2019
mict_newin 1084
mict_helper1 7529
mict_newin 1084
mict_restofloop 1129
mict_totalloop 15982
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 43052
Timing BFC loop total: 264049
bfc 1
Localtime: Mon Jun 15 17:09:24 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 40
Localtime: Mon Jun 15 17:09:24 2015
Unused reads: 1551393
bfc 8/0
0 Known 1: 1005
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 452
pft 11 / 118
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 637
pft 12 / 122
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 738
pft 14 / 132
[181] +++++++++++++++++++++++++++++++++++++++++++a++++++++++++++++ 1013
pft 12 / 126
[240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1195
pft 10 / 119
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1336
pft 12 / 129
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1510
pft 11 / 133
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1670
pft 13 / 131
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1718
pft 16 / 133
[540] ++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1818
pft 21 / 151
[599] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1859
pft 19 / 124
[659] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1893
pft 20 / 115
[719] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 1915
pft 22 / 94
[778] ++++++++a+++++++++a+a++a++++++++++++++++++aa++++++++++++++++ 1950
pft 20 / 87
[832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++a+ 1979
pft 20 / 77
[890] +++++++++++++++++++++++aa+++++++++++++++++++++++++++++++++++ 2359
pft 12 / 122
[948] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2615
pft 9 / 122
[1008] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2694
pft 13 / 124
[1068] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2713
pft 15 / 115
[1128] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 2747
pft 20 / 100
[1186] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3171
pft 14 / 102
[1246] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3302
pft 11 / 122
[1306] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3473
pft 14 / 145
[1366] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3568
pft 15 / 126
[1426] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3631
pft 13 / 129
[1486] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3916
pft 14 / 119
[1546] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4004
pft 13 / 126
[1606] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4018
pft 15 / 130
[1666] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 4031
pft 14 / 124
[1725] ++++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++ 4185
pft 14 / 100
[1784] ++++++++++++++++++++++++++++++++++++++++++++++++a+aa++++++++ 4198
pft 12 / 145
[1841] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4201
pft 12 / 154
[1901] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4210
pft 16 / 159
[1961] +++++++++++++++++a+++++++++a+a++++++++++++++++++++++++++++++ 4220
pft 34 / 154
[2018] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4223
pft 34 / 109
[2078] ++++++++++++++++++aa+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaapriv_ld addRead:
269276
priv_ld total: 299205
Timing BFC paf construct: 299253

ccon timings:
cct pre 1533
cct dir 2012
cct xcu 8001
cct tmp 1104
cct sw 165089
cct pic 1188
cct ico 73756
cct icm 0
cct upd 1301
cct del 0
cct rmz 1263
cct gcp 206

ccon i timings (2095):
ccit insglcc 222
ccit insglaro 696
ccit insglact 89
ccit insgltot 2549
ccit pr 13318
ccit templ 1755
ccit index 1162
ccit biglccins 2575
ccit biglinterpol 468
ccit biglupdtags 286
ccit biglfpcri 267
ccit bigllgap 11831
ccit biglshiftread 2577
ccit bigltot 32188
ccit insgr 1143
ccit ucv 11390

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2096
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:24 2015
Timing BFC analysereadcov: 9488
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 69
mict_fallout 4337
mict_newin 2264
mict_helper1 17452
mict_newin 2264
mict_restofloop 2304
mict_totalloop 35346
done.

-------------- Contig statistics ----------------
Contig id: 40
Contig length: 4223

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2096 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 174 0 0
0 0 0
Avg. coverage 0.000 0.000 95.581 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 174
Avg. contig coverage: 95.581

Consensus contains: A: 569 C: 1198 G: 1248 T: 706 N: 0
IUPAC: 0 Funny: 0 *: 502
GC content: 65.735%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 35761
Localtime: Mon Jun 15 17:09:24 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 42669 cases.

P 1, marked 42669 reads.
Timing BFC edit tricky1: 25528
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 29547
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 807 cases.

Edited 807 reads.
Localtime: Mon Jun 15 17:09:25 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:25 2015
Timing BFC edit tricky2: 19419

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 171 positions.
Localtime: Mon Jun 15 17:09:25 2015
Deleting superfluous gap columns (2) ... done, deleted 291 columns.
Localtime: Mon Jun 15 17:09:25 2015
Timing BFC edit single discrepancy, no HAF: 41143
bfc 12/0
Timing BFC delPSHP: 329
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 11965
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 276
mict_pre 7
mict_shadow 67
mict_fallout 4236
mict_newin 2151
mict_helper1 17186
mict_newin 2151
mict_restofloop 2242
mict_totalloop 34393
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 85193
Timing BFC loop total: 558949
bfc 1
Localtime: Mon Jun 15 17:09:25 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 41
Localtime: Mon Jun 15 17:09:25 2015
Unused reads: 1549297
bfc 8/0
0 Known 1: 2096
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 474
pft 10 / 119
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 585
pft 12 / 126
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 905
pft 16 / 133
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 994
pft 16 / 125
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1246
pft 13 / 115
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1496
pft 12 / 115
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1545
pft 15 / 119
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1593
pft 15 / 127
[481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1848
pft 14 / 112
[541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1987
pft 11 / 127
[601] +++++++++++++++++++a++++++++++++++a+++++++++++++++++++++++++ 2055
pft 14 / 128
[659] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2092
pft 12 / 130
[719] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2128
pft 15 / 106
[779] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2473
pft 12 / 113
[839] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 2539
pft 16 / 142
[898] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2595
pft 12 / 136
[958] ++++++++a+++++++++a++++++++++++++a++++++++++++++++++++++++++ 2779
pft 14 / 116
[1015] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2968
pft 11 / 123
[1075] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 3019
pft 17 / 115
[1134] +++++++++++++++++++++++++++++++++++++++a++a++da+++++++++++++ 3027
pft 14 / 120
[1190] +a++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3379
pft 15 / 123
[1248] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3462
pft 12 / 127
[1308] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3540
pft 15 / 119
[1368] ++++++++++++a+++++++++++++++++++++++++++++++++++++a++++++++a 3591
pft 16 / 108
[1425] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3763
pft 13 / 107
[1485] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3985
pft 11 / 125
[1545] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4171
pft 9 / 125
[1605] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4184
pft 18 / 129
[1665] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4519
pft 17 / 115
[1725] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4817
pft 12 / 121
[1785] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 4844
pft 16 / 85
[1844] ++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5046
pft 12 / 137
[1903] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5102
pft 12 / 137
[1963] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5383
pft 12 / 125
[2023] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5556
pft 11 / 122
[2083] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5613
pft 14 / 125
[2143] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 5684
pft 18 / 126
[2202] ++++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++ 5693
pft 17 / 119
[2261] ++++a++a++++++++++a+++++++++++++a++++++++a++++++++++++++++a+ 5699
pft 15 / 100
[2315] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++a+++ 5802
pft 13 / 152
[2373] +++++++++++++++++++a++++++++++++a++++++++++++++++++a++++++++ 5813
pft 12 / 152
[2430] ++a+a+++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5814
pft 21 / 156
[2488] ++a+++++++++++++++++++++++++++++a+++++++++++d+++++++++++++a+ 5824
pft 28 / 149
[2544] +++++++++++++++++++++++++++++++++++++++++++aaa+++++++++a++++ 5832
pft 23 / 125
[2600] ++++++++++++++++++++++d+++++++++a+++++++++++++++++++++++a+++ 5837
pft 23 / 96
[2657] +++++++++++++++++++++++++++++++++++++++++++++++++a++++++++++ 5844
pft 20 / 106
[2716] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5851
pft 22 / 126
[2776] ++++++++++a++++a+++++a++++++++++++++++++++++++++++++++++++++ 5854
pft 30 / 110
[2833] +aaaaaaaa++aa+++++a++a++aaaaadaa+aaaaaaa+aapriv_ld addRead: 366412
priv_ld total: 407758
Timing BFC paf construct: 407816

ccon timings:
cct pre 2102
cct dir 3198
cct xcu 13490
cct tmp 1563
cct sw 224912
cct pic 1575
cct ico 96965
cct icm 0
cct upd 1804
cct del 0
cct rmz 1729
cct gcp 329

ccon i timings (2845):
ccit insglcc 281
ccit insglaro 963
ccit insglact 129
ccit insgltot 3527
ccit pr 17933
ccit templ 2493
ccit index 1514
ccit biglccins 3092
ccit biglinterpol 551
ccit biglupdtags 328
ccit biglfpcri 317
ccit bigllgap 15243
ccit biglshiftread 2915
ccit bigltot 40506
ccit insgr 1587
ccit ucv 15591

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2846
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:25 2015
Timing BFC analysereadcov: 13044
makeIntelligentConsensus() complete calc .. mict_fin 0
mict_pre 7
mict_shadow 98
mict_fallout 6203
mict_newin 3256
mict_helper1 24926
mict_newin 3256
mict_restofloop 3293
mict_totalloop 50658
done.

-------------- Contig statistics ----------------
Contig id: 41
Contig length: 5858

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2846 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 183 0 0
0 0 0
Avg. coverage 0.000 0.000 93.358 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 183
Avg. contig coverage: 93.358

Consensus contains: A: 898 C: 1722 G: 1746 T: 891 N: 0
IUPAC: 0 Funny: 0 *: 601
GC content: 65.969%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 51477
Localtime: Mon Jun 15 17:09:25 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 52351 cases.

P 1, marked 52351 reads.
Timing BFC edit tricky1: 32886
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 38523
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 321 positions.
Localtime: Mon Jun 15 17:09:25 2015
Deleting superfluous gap columns (2) ... done, deleted 88 columns.
Localtime: Mon Jun 15 17:09:25 2015
Timing BFC edit single discrepancy, no HAF: 37636
bfc 12/0
Timing BFC delPSHP: 423
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: 210
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 209
mict_pre 6
mict_shadow 80
mict_fallout 6003
mict_newin 3162
mict_helper1 24042
mict_newin 3162
mict_restofloop 3261
mict_totalloop 48955
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 126077
Contig coverage analysis ... Timing BFC loop total: 709748
bfc 1
Localtime: Mon Jun 15 17:09:25 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 42
Localtime: Mon Jun 15 17:09:25 2015
Unused reads: 1546451
bfc 8/0
0 Known 1: 2846
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 415
pft 11 / 124
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 554
pft 16 / 136
[121] +++++++++a+++++a+++++++++++++++++++a+++++a++++++++++++++++++ 608
pft 15 / 122
[177] ++++a++++++++++++++++++++++++++++++++++a++++++++++++++++++++ 702
pft 16 / 109
[235] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 902
pft 12 / 110
[295] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 948
pft 12 / 118
[355] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 980
pft 14 / 103
[415] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1395
pft 9 / 114
[475] +++a+++++++++++++++++++++++++++++++++++++++++++a++++++++++++ 1472
pft 14 / 87
[533] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 1889
pft 12 / 91
[592] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2135
pft 13 / 111
[652] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2228
pft 11 / 132
[712] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2244
pft 22 / 123
[772] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2467
pft 21 / 83
[832] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2624
pft 12 / 124
[892] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2688
pft 20 / 137
[952] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2887
pft 11 / 112
[1012] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2954
pft 12 / 130
[1072] +++++++++++++++++++++++++a++++++++++++++++++++++++++++++++++ 3507
pft 12 / 129
[1131] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3818
pft 11 / 109
[1191] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3895
pft 12 / 136
[1251] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3908
pft 15 / 126
[1311] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3933
pft 16 / 132
[1371] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3943
pft 13 / 120
[1431] +++++++++++++++++++++++++++++++++++++++++++++++++++d++++++++ 3981
pft 13 / 118
[1490] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4306
pft 10 / 123
[1550] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4506
pft 9 / 125
[1610] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4565
pft 14 / 144
[1670] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4622
pft 14 / 123
[1730] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4843
pft 11 / 123
[1790] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5160
pft 11 / 121
[1850] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5315
pft 11 / 117
[1910] +++++++++++++++++++++++++++++a++++++++++++++++++++++++++++++ 5334
pft 14 / 127
[1969] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5350
pft 17 / 116
[2029] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 5358
pft 16 / 106
[2088] ++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++ 5366
pft 16 / 117
[2147] ++++++++++++++++++++++++++++++++++++++++++++a+++++++++++++++ 5376
pft 12 / 135
[2206] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5376
pft 12 / 156
[2266] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 5381
pft 21 / 168
[2325] ++++++++++++++++++++++a++++++++++++++++++++++a+++++++++++++a 5387
pft 24 / 155
[2382] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5390
pft 27 / 129
[2442] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5398
pft 19 / 129
[2502] +++++a++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5404
pft 26 / 107
[2561] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5407
pft 22 / 91
[2621] ++++++++++++++++++++++++aa++++++++++++++a+++++++++++++++++++ 5415
pft 32 / 130
[2678] ++aaaa+aaaa+aaaapriv_ld addRead: 338189
priv_ld total: 374686
Timing BFC paf construct: 374749

ccon timings:
cct pre 1946
cct dir 3106
cct xcu 11795
cct tmp 1429
cct sw 207033
cct pic 1491
cct ico 90453
cct icm 0
cct upd 1715
cct del 0
cct rmz 1635
cct gcp 154

ccon i timings (2680):
ccit insglcc 118
ccit insglaro 380
ccit insglact 45
ccit insgltot 2276
ccit pr 16733
ccit templ 2315
ccit index 1421
ccit biglccins 2859
ccit biglinterpol 544
ccit biglupdtags 309
ccit biglfpcri 286
ccit bigllgap 14189
ccit biglshiftread 2634
ccit bigltot 38521
ccit insgr 1564
ccit ucv 14491

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2681
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:26 2015
Timing BFC analysereadcov: 12235
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 88
mict_fallout 5689
mict_newin 3020
mict_helper1 22953
mict_newin 3020
mict_restofloop 3081
mict_totalloop 46441
done.

-------------- Contig statistics ----------------
Contig id: 42
Contig length: 5419

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2681 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 174 0 0
0 0 0
Avg. coverage 0.000 0.000 93.927 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 174
Avg. contig coverage: 93.927

Consensus contains: A: 848 C: 1642 G: 1512 T: 825 N: 0
IUPAC: 0 Funny: 0 *: 592
GC content: 65.341%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 47108
Localtime: Mon Jun 15 17:09:26 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 52273 cases.

P 1, marked 52273 reads.
Timing BFC edit tricky1: 32435
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 34729
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 940 cases.

Edited 940 reads.
Localtime: Mon Jun 15 17:09:26 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:26 2015
Timing BFC edit tricky2: 25599

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 265 positions.
Localtime: Mon Jun 15 17:09:26 2015
Deleting superfluous gap columns (2) ... done, deleted 365 columns.
Localtime: Mon Jun 15 17:09:26 2015
Timing BFC edit single discrepancy, no HAF: 53458
bfc 12/0
Timing BFC delPSHP: 493
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 14444
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 360
mict_pre 6
mict_shadow 82
mict_fallout 5301
mict_newin 2791
mict_helper1 21294
mict_newin 2791
mict_restofloop 2840
mict_totalloop 43481
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 108895
Contig coverage analysis ... Timing BFC loop total: 705848
bfc 1
Localtime: Mon Jun 15 17:09:26 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 43
Localtime: Mon Jun 15 17:09:26 2015
Unused reads: 1543770
bfc 8/0
0 Known 1: 2681
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 514
pft 11 / 116
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 700
pft 16 / 134
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 778
pft 17 / 130
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 821
pft 17 / 113
[241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 869
pft 19 / 99
[301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1026
pft 18 / 93
[361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1287
pft 17 / 108
[421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1360
pft 14 / 137
[481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1424
pft 13 / 134
[541] +++++++a++++++++++++++++++++++++++++++++++++++++++++++++++++ 1749
pft 12 / 127
[600] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1829
pft 14 / 127
[660] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1895
pft 13 / 115
[720] ++++++++++aa++++++++++++++++++++++++++++++++++++++++++++++++ 1903
pft 13 / 116
[777] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2022
pft 15 / 119
[837] ++++++++++++++++++++d++++++++++++++++++++++++++++++++++++a++ 2070
pft 15 / 159
[895] ++++++++++++a+++++++++a+++++++++++++++++d+a+++++++++++++++++ 2087
pft 11 / 154
[951] ++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++ 2093
pft 29 / 134
[1010] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2325
pft 21 / 116
[1070] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2454
pft 12 / 119
[1130] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2553
pft 11 / 131
[1190] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3009
pft 9 / 111
[1250] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3148
pft 11 / 121
[1310] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3379
pft 11 / 122
[1370] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3410
pft 16 / 135
[1430] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3492
pft 18 / 116
[1490] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 3601
pft 24 / 117
[1549] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3668
pft 17 / 91
[1609] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++aa+ 3681
pft 16 / 91
[1667] +++++a++++++++++++++++++++++++++a+++++++++++++++++a++++++++a 3889
pft 16 / 115
[1723] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4201
pft 10 / 122
[1782] ++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++++ 4301
pft 10 / 129
[1841] +++++++++++++++++++a+++++++++++++++a++++++++++++++++++++++++ 4329
pft 11 / 130
[1898] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4391
pft 14 / 99
[1958] +a+++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 4393
pft 15 / 94
[2016] +++++++++++++++++++a+a++++a++++++a+a++++++++a+++++++++++++a+ 4649
pft 10 / 98
[2069] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4658
pft 13 / 139
[2129] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4669
pft 23 / 135
[2189] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4671
pft 19 / 141
[2249] ++++++++a++++++++++++++++++++++++a++++++a++++a++++++++++a+a+ 4679
pft 29 / 172
[2303] ++++++++++++++++a++++++++++++++a++++++++++++++++++++++++++++ 4685
pft 31 / 123
[2361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4691
pft 20 / 156
[2421] +a++++++++++++++++++++++++++++++++++++++++++++++++++a+a+++++ 4695
pft 29 / 121
[2478] ++++++++++++++++++++++++++++G++a+++++GGGG++++++++++G+++++G++ 4706
pft 16 / 132
[2529] G++++a++G++++++G++++G+++++++G+++++G+++++++++a++G+++G+++GG+G+ 4716
pft 17 / 142
[2577] ++GG+++++++G++++++++G++++GG+++++++G+++++G+++++++GG+++++++G++ 4724
pft 23 / 126
[2625] G+++++GG++++++++++G++++GGGGGGGGG+++G+++GGG++G+++++++++++++++ 4728
pft 21 / 104
[2668] ++++++G+GGG++GG+G++G+GG++++++G+++G+++G++GGGGGG++GGGGG++a+GGG 4730
pft 21 / 79
[2700] +G+G++GG++G++++++G+++++++++GGaGGG+a+++GGGG+GGGG+++++++G+++++ 4736
pft 26 / 80
[2738] ++++Ga++++G++++G+++GGG+G+++G++GGG+GG++++GG++aaaaaaaaaaaaaada 4736
pft 121 / 71
[2766] +aaaaaaaaGaaGGGGGGGGGaGGaGGaaGGGGGGGGGGGGGGGGGGGGGaGGaGGGGGG 4738
pft 5 / 114
[2766] GGGGGaGGGGGGGGGGGaGGGGGG+aGGGGGGGGGGGGGGGGGGGGGGGGGGGpriv_ld addRead:
371934
priv_ld total: 424974
Timing BFC paf construct: 425026

ccon timings:
cct pre 2237
cct dir 3829
cct xcu 13565
cct tmp 1657
cct sw 230166
cct pic 1596
cct ico 95380
cct icm 0
cct upd 1744
cct del 0
cct rmz 1692
cct gcp 875

ccon i timings (2766):
ccit insglcc 58
ccit insglaro 187
ccit insglact 25
ccit insgltot 1866
ccit pr 17071
ccit templ 2473
ccit index 1433
ccit biglccins 2975
ccit biglinterpol 570
ccit biglupdtags 351
ccit biglfpcri 336
ccit bigllgap 15542
ccit biglshiftread 2366
ccit bigltot 42554
ccit insgr 1609
ccit ucv 14686

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 2767
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:26 2015
Timing BFC analysereadcov: 12313
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 7
mict_shadow 97
mict_fallout 5181
mict_newin 2562
mict_helper1 22135
mict_newin 2562
mict_restofloop 2627
mict_totalloop 42509
done.

-------------- Contig statistics ----------------
Contig id: 43
Contig length: 4738

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 2767 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 231 0 0
0 0 0
Avg. coverage 0.000 0.000 108.343 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 231
Avg. contig coverage: 108.343

Consensus contains: A: 651 C: 1296 G: 1378 T: 798 N: 0
IUPAC: 0 Funny: 0 *: 615
GC content: 64.856%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 43033
Localtime: Mon Jun 15 17:09:27 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 58725 cases.

P 1, marked 58725 reads.
Timing BFC edit tricky1: 34122
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 38814
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 267 positions.
Localtime: Mon Jun 15 17:09:27 2015
Deleting superfluous gap columns (2) ... done, deleted 92 columns.
Localtime: Mon Jun 15 17:09:27 2015
Timing BFC edit single discrepancy, no HAF: 36287
bfc 12/0
Timing BFC delPSHP: 462
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: 286
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 161
mict_pre 6
mict_shadow 80
mict_fallout 5314
mict_newin 2581
mict_helper1 22188
mict_newin 2581
mict_restofloop 2641
mict_totalloop 42938
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 119446
Timing BFC loop total: 712969
bfc 1
Localtime: Mon Jun 15 17:09:27 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 44
Localtime: Mon Jun 15 17:09:27 2015
Unused reads: 1541003
bfc 8/0
0 Known 1: 2767
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 645
pft 12 / 136
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 855
pft 11 / 123
[121] +++++++++++++++++++a++++++++++++a+++++aa++++++++++++++++++++ 880
pft 15 / 124
[177] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 893
pft 16 / 109
[237] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++a+ 952
pft 18 / 97
[296] +++++++++++++++a++++++++++++++++++++++++++++++++++++++++++++ 1207
pft 13 / 100
[355] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1485
pft 11 / 118
[415] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1638
pft 16 / 120
[475] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1699
pft 13 / 117
[535] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1748
pft 15 / 119
[595] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1796
pft 16 / 108
[655] ++++++++++++++++++a++++++++++d++++++++++++++++++++++++++++++ 1867
pft 15 / 110
[713] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2325
pft 10 / 115
[773] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2507
pft 13 / 142
[833] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2637
pft 14 / 123
[893] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2672
pft 16 / 127
[953] +++++++++++++++a++++++++++a+++++++++a++++a++++++a+++++++++++ 2727
pft 21 / 115
[1008] +++++++++++++++++++++++++++++++++++++++a++++++++++++a+++++++ 2936
pft 20 / 76
[1066] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3170
pft 13 / 101
[1126] +++++++d++++++++++++++++++a++++++++++++++++++++++++a+++a++++ 3178
pft 9 / 142
[1182] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3630
pft 10 / 115
[1242] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3887
pft 11 / 123
[1302] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3953
pft 14 / 132
[1362] ++++++++++++++++++++++++++++++a++++++a++++++++++++++++++++++ 3992
pft 16 / 120
[1420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4083
pft 15 / 113
[1480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4374
pft 11 / 114
[1540] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 4388
pft 13 / 112
[1599] ++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++++ 4645
pft 11 / 119
[1658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5273
pft 9 / 106
[1718] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5598
pft 12 / 105
[1778] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5889
pft 11 / 113
[1838] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6055
pft 12 / 129
[1898] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6252
pft 11 / 123
[1958] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6352
pft 12 / 122
[2018] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6379
pft 16 / 138
[2078] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6677
pft 13 / 119
[2138] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6737
pft 21 / 107
[2198] ++++++++++++++++++++a++++++++++++++++++++++++a++++++++++++++ 6813
pft 18 / 104
[2256] ++++++++++a++++a++++++++++++++++++++++++++++++++++++++++++++ 6826
pft 23 / 97
[2314] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7158
pft 15 / 135
[2374] +++++++++++++++++++++++a++++++++++++++++++++++++++++++++++++ 7294
pft 13 / 129
[2433] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7306
pft 18 / 108
[2493] +++++++a+++++++++++++++++++++++++++++++++++++a++++++++++++++ 7312
pft 21 / 91
[2551] ++++++++++++++++++++++++++++++++a+++a++++++++++++++++++a++++ 7319
pft 16 / 99
[2608] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 7585
pft 14 / 112
[2667] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7669
pft 14 / 86
[2727] ++++++++++++++++++++a+++++++++++++++++++++a+++++++++++++++++ 7693
pft 13 / 156
[2785] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7696
pft 14 / 151
[2845] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7706
pft 19 / 165
[2905] +++++++++++++a++++++++++++++++++++++++a++++++++++++++++++++a 7718
pft 20 / 159
[2962] ++++++a+++++++++++++++++a+++++++++++++++++++++++++++++++++++ 7725
pft 22 / 167
[3020] +++++a++++++++++++++++++++++++a+++++++++++++++++++++++++++++ 7732
pft 20 / 134
[3078] ++++++++a+++++++++++a+++++++++++++++++++++++++++++++++++a+++ 7736
pft 27 / 110
[3135] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7743
pft 24 / 144
[3195] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 7749
pft 31 / 146
[3255] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 7756
pft 46 / 118
[3313] aaaaaaaaaaaaaaaaaaaaaaaaa+aaaaaaaaapriv_ld addRead: 416735
priv_ld total: 465119
Timing BFC paf construct: 465192

ccon timings:
cct pre 2485
cct dir 4710
cct xcu 13318
cct tmp 1810
cct sw 250753
cct pic 1853
cct ico 115559
cct icm 0
cct upd 2075
cct del 0
cct rmz 2009
cct gcp 331

ccon i timings (3313):
ccit insglcc 146
ccit insglaro 465
ccit insglact 61
ccit insgltot 2807
ccit pr 20764
ccit templ 2968
ccit index 1778
ccit biglccins 6179
ccit biglinterpol 767
ccit biglupdtags 447
ccit biglfpcri 431
ccit bigllgap 18483
ccit biglshiftread 3547
ccit bigltot 51405
ccit insgr 2043
ccit ucv 17693

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 3314
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:27 2015
Timing BFC analysereadcov: 14936
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 9
mict_shadow 106
mict_fallout 7504
mict_newin 4214
mict_helper1 28702
mict_newin 4214
mict_restofloop 4355
mict_totalloop 61406
done.

-------------- Contig statistics ----------------
Contig id: 44
Contig length: 7758

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 3314 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 202 0 0
0 0 0
Avg. coverage 0.000 0.000 80.007 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 202
Avg. contig coverage: 80.007

Consensus contains: A: 1275 C: 2327 G: 2300 T: 1034 N: 0
IUPAC: 0 Funny: 0 *: 822
GC content: 66.710%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 62357
Localtime: Mon Jun 15 17:09:27 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 65169 cases.

P 1, marked 65169 reads.
Timing BFC edit tricky1: 40782
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 43678
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Checking for allowed edits in 1234 cases.

Edited 1234 reads.
Localtime: Mon Jun 15 17:09:27 2015
Deleting superfluous gap columns (1) ... done, deleted 0 columns.
Localtime: Mon Jun 15 17:09:27 2015
Timing BFC edit tricky2: 29991

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 285 positions.
Localtime: Mon Jun 15 17:09:27 2015
Deleting superfluous gap columns (2) ... done, deleted 510 columns.
Localtime: Mon Jun 15 17:09:28 2015
Timing BFC edit single discrepancy, no HAF: 72193
bfc 12/0
Timing BFC delPSHP: 671
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 17993
Done.
bfc 17/0
I have newreptmarked 0 wasmajorovercalledited 1 contignotok 0 continueiter: 0
Had many overcall edits in reads.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 510
mict_pre 6
mict_shadow 97
mict_fallout 6840
mict_newin 3922
mict_helper1 26029
mict_newin 3922
mict_restofloop 3974
mict_totalloop 55992
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 135948
Contig coverage analysis ... Timing BFC loop total: 885991
bfc 1
Localtime: Mon Jun 15 17:09:28 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 45
Localtime: Mon Jun 15 17:09:28 2015
Unused reads: 1537689
bfc 8/0
0 Known 1: 3314
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++ 428
pft 12 / 119
[60] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 460
pft 12 / 117
[120] +++++++++++++++++++++++++++++++++++++++++++++++++++++++a++++ 539
pft 13 / 116
[179] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 927
pft 12 / 121
[239] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 996
pft 10 / 130
[299] +++a+++++++++++++++++++++++++++++++a++++++++a++++++a+++++a++ 1290
pft 10 / 113
[354] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1600
pft 10 / 116
[414] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1739
pft 12 / 117
[474] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1782
pft 15 / 127
[534] +++++++++++++++++++++++++++++++++++++++a+a++a+++++++++++++++ 1852
pft 17 / 109
[591] +++a++++++++++++a++++aaaa+++++++++++++aa+a+a+++++++++a+aa++a 1865
pft 13 / 84
[637] ++a+++aa++++aaa++++++++++a+++++aaa+aa++++aa+++++++++++++++++ 1915
pft 13 / 99
[683] +++++++a++++++aa+d+++++++++a+++aa+++++++++++++++++++++++++++ 2047
pft 13 / 143
[736] ++++++++++++++++++++++++a+++++++++++++++++++++++a+++++++++++ 2258
pft 10 / 131
[794] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2363
pft 9 / 125
[854] +a++++++++++++a++++++++++++++aa++aa++++++++aa+++a+++++++++++ 2369
pft 14 / 155
[905] +++a++++++++++aa++++++a++a++++++++a+++++++++++++++++++++++++ 2380
pft 14 / 152
[959] +a++++++++++++++++++++++++a++++++++++++++a+++++a++++a+++++++ 2394
pft 22 / 149
[1014] +a++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2399
pft 22 / 126
[1073] +++++++++++++++++++++++++++++++++++++++++a++++++++++++++++++ 2408
pft 21 / 109
[1132] ++++++++++++++++++++++a+++++++++GG+G+++++++++++++++++++++++G 2422
pft 18 / 112
[1186] GGG+G+G++G++G++G+++G++++++GGG++++da+++++++++++++++++++++++++ 2765
pft 12 / 116
[1233] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2947
pft 11 / 121
[1293] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2985
pft 15 / 110
[1353] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2995
pft 15 / 105
[1413] ++++++++++++++++++++++++++++++++++++++++++d+++++++++++++++++ 3321
pft 12 / 115
[1472] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3536
pft 10 / 129
[1532] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3545
pft 17 / 162
[1592] ++++++++++++++++++++a+++++++++++++++++++++++++aa+++++++a++++ 3549
pft 12 / 119
[1648] ++++++++++++++++++++a+++++++++++++++++++++++++++++++++++++++ 3824
pft 11 / 123
[1707] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3889
pft 11 / 128
[1767] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3934
pft 10 / 135
[1827] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4109
pft 13 / 139
[1887] ++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++a+ 4118
pft 12 / 146
[1945] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4235
pft 19 / 147
[2005] +++++++++++++++++++++++++++++++++++++++++++++++++++aaa++++++ 4259
pft 10 / 133
[2062] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4265
pft 28 / 140
[2122] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4266
pft 14 / 155
[2182] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4271
pft 25 / 178
[2242] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4283
pft 27 / 158
[2301] a+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4289
pft 33 / 108
[2361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4642
pft 13 / 137
[2421] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 4745
pft 13 / 125
[2481] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5047
pft 10 / 131
[2541] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5265
pft 11 / 128
[2601] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5396
pft 10 / 135
[2661] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5411
pft 12 / 138
[2721] ++++++++++++++++++++++++++++++++++++++++++++++++++++a+++++++ 5456
pft 12 / 127
[2780] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 5696
pft 11 / 127
[2840] +++++++++++++++++++++++++++++++++++a++++++++++++++++a+++++++ 5775
pft 15 / 166
[2898] +++++++++++a+a++++++a+++++++++++++++++++++++++++++++++++++++ 5853
pft 15 / 109
[2955] +++++++++++++++++++++++++++++++++++++++++++++aaaa+++++++++++ 6063
pft 18 / 101
[3011] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6284
pft 11 / 120
[3071] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6529
pft 10 / 134
[3131] +++++++++++++++++++++++++++++++++++++++++++++++++++a+a++++++ 6581
pft 17 / 135
[3189] ++++++++++++++++++++++++++++++++++++++++++++++++a+++++++++++ 6642
pft 15 / 109
[3248] ++a+aa++++++a+++++++++++++++++++++++++++++++a+++++++++++++++ 6779
pft 12 / 109
[3303] +a++++++++++++++++++++++++++++++++a++a+++++++++++++a++++++++ 6792
pft 16 / 101
[3359] +++++++++++++++++++++++++++++++++++++++++++aa+++++++++++++++ 6815
pft 11 / 163
[3417] ++++++++++++++++++a+++++++a+++++++++++++++++++++++++++++++++ 6823
pft 20 / 135
[3475] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6831
pft 13 / 146
[3535] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6837
pft 17 / 166
[3595] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6843
pft 27 / 156
[3655] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6849
pft 22 / 160
[3715] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6854
pft 20 / 175
[3775] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 6856
pft 24 / 151
[3835] ++++++++++++++++++++++++++++++++a+++++++++++++++++++++++++++ 6864
pft 44 / 141
[3894] +++++++++++++++++++++++++++++++++++a++++++++++++++++++++++++ 6866
pft 63 / 96
[3953] +++++a++++++++++++++++++++++++++++++++++++++++++++aaaaaaaaa+ 6875
pft 133 / 92
[4002] aaaaaaaaaaaaaaaaaaa+++a+a+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa 6879
pft 4 / 121
[4008] ++++a+aa++++++++aa+aaaa+aaaaaaaaaaaaaapriv_ld addRead: 562361
priv_ld total: 629344
Timing BFC paf construct: 629411

ccon timings:
cct pre 3100
cct dir 5175
cct xcu 22072
cct tmp 2223
cct sw 346751
cct pic 2254
cct ico 148015
cct icm 0
cct upd 2540
cct del 0
cct rmz 2476
cct gcp 696

ccon i timings (4021):
ccit insglcc 299
ccit insglaro 910
ccit insglact 122
ccit insgltot 4065
ccit pr 25692
ccit templ 3676
ccit index 2184
ccit biglccins 5691
ccit biglinterpol 831
ccit biglupdtags 475
ccit biglfpcri 442
ccit bigllgap 24678
ccit biglshiftread 4656
ccit bigltot 68071
ccit insgr 2250
ccit ucv 22474

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 4022
bfc 9/0


Finished building.
Localtime: Mon Jun 15 17:09:28 2015
Timing BFC analysereadcov: 18806
makeIntelligentConsensus() complete calc .. mict_fin 1
mict_pre 8
mict_shadow 137
mict_fallout 7858
mict_newin 3722
mict_helper1 33889
mict_newin 3722
mict_restofloop 3812
mict_totalloop 63840
done.

-------------- Contig statistics ----------------
Contig id: 45
Contig length: 6888

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 4022 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 266 0 0
0 0 0
Avg. coverage 0.000 0.000 115.407 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 266
Avg. contig coverage: 115.407

Consensus contains: A: 1074 C: 1999 G: 1934 T: 981 N: 0
IUPAC: 1 Funny: 0 *: 899
GC content: 65.681%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 64611
Localtime: Mon Jun 15 17:09:28 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Marking tricky overcall runs in 92502 cases.

P 1, marked 92502 reads.
Timing BFC edit tricky1: 56260
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step 2:
Found
- 1 new Strong RMB (SRMc)
- 0 new Weak RMB (WRMc)
- 0 SNP
positions tagged.Timing BFC mark reps: 56084
bfc 11/0

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 470 positions.
Localtime: Mon Jun 15 17:09:29 2015
Deleting superfluous gap columns (2) ... done, deleted 139 columns.
Localtime: Mon Jun 15 17:09:29 2015
Timing BFC edit single discrepancy, no HAF: 63139
bfc 12/0
Timing BFC delPSHP: 935
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: 245
Done.
bfc 17/0
I have newreptmarked 1 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Identified misassembled reads in contig.

Accepting probably misassembled contig, keeping as is.
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 349
mict_pre 7
mict_shadow 117
mict_fallout 7808
mict_newin 3644
mict_helper1 33881
mict_newin 3644
mict_restofloop 3712
mict_totalloop 63746
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving temp CAF ... done.
done.
Timing BFC store con: 183251
Contig coverage analysis ... Timing BFC loop total: 1076061
bfc 1
Localtime: Mon Jun 15 17:09:29 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 46
Localtime: Mon Jun 15 17:09:29 2015
Unused reads: 1533667
bfc 8/0
0 Known 1: 4022
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 481
pft 11 / 116
[61] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 677
pft 13 / 132
[121] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 745
pft 14 / 126
[181] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 826
pft 16 / 129
[241] ++++++a+++++++++++++++++++++++++++++++++++++++++++++++++++++ 1076
pft 18 / 115
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1187
pft 12 / 125
[360] +++++++++++++++++++++++++++a++++++++++++++a+++++++++++++++++ 1241
pft 15 / 152
[418] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1301
pft 13 / 112
[478] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1617
pft 14 / 113
[538] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1709
pft 14 / 122
[598] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1763
pft 14 / 124
[658] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1790
pft 16 / 117
[718] +++++++++++++++++++++++++++++++++++++++++++++a++++++++++++++ 1867
pft 15 / 125
[777] ++++++++++++++++++++++++++++++++++++++++a++a++++++++++++++++ 2039
pft 14 / 108
[835] ++++++++a++++++++++++++++++++++a++++++++++++++++++++++++++++ 2065
pft 13 / 138
[893] ++++++++++++++++++++++++++++a+++++++++++++++++++++++++++++++ 2073
pft 11 / 151
[952] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2080
pft 27 / 150
[1012] ++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++ 2091
pft 27 / 111
[1071] ++++aG+++GG+GG++G++G+++++G++++++++++++++++++++++++++++++++++ 2394
pft 12 / 126
[1122] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2489
pft 12 / 128
[1182] ++++++++++++++++++++++++++++++++++++a+++++++++++++++++++++++ 2732
pft 11 / 124
[1241] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2776
pft 11 / 130
[1301] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2860
pft 11 / 135
[1361] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2876
pft 12 / 141
[1421] +++++++++++++++++++++++++++G++++++G++++++GGGG++++GGGGG+GG+GG 2882
pft 14 / 122
[1466] ++++++GG+G+++++++++++++++G++++++++++++++++++++++++++++++++++ 2887
pft 21 / 130
[1522] +++++++GGGG++GGGGGGG+GGG+GG+++++GG++G+G++++++G+G+++GG+++++++ 2893
pft 11 / 103
[1557] G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 2896
pft 19 / 159
[1617] +++++++++++++++++++++a++++++++++++++++++++++++++++++++++++++ 2901
pft 29 / 143
[1676] +++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++ 2909
pft 17 / 160
[1735] +++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++ 3095
pft 24 / 153
[1794] +++++++++++++++++++++++++++++++++++++++++++++++++++++++++a++ 3100
pft 29 / 106
[1853] ++++++++++++++++++++++++++GG+GGGGGGGG+GGG++GGGG+G++GG++++++G 3104
pft 17 / 102
[1892] +++++++++++++++++++++++++++++++++++++++++++GG+++G+++++++G++G 3118
pft 13 / 129
[1946] G+++G++GG+GG+G+++++++Ga+GGG++++++G++G++G+G+++G+GGG+++G+++G+G 3124
pft 14 / 121
[1984] +++++++G++G++G+G+GG+G+GG++++GGG+++G+++GGGGG++GGGGGG++G++GGG+ 3135
pft 12 / 119
[2015] G+G+GGGG+G++GGGG++++GG++++G++GG+++GG+GG++GG++G+++G++++G+G++G 3139
pft 18 / 101
[2049] +G+G+++G+++++G++GGG+G++Ga+++G++G+G+GG+GGGGGGGGGGGGGG++GG+++a 3142
pft 20 / 79
[2077] ++G+G++GG+GGGGGGGGGGGG++++GGGGGGGGGGGGG+++GG+++++Ga++a+GG+GG 3147
pft 18 / 77
[2098] GG+G+++++aG++GGGG+++++G+GGGG+G+GG+GGG+GG+GG+++GGGGGGGGGG+GG+ 3149
pft 18 / 65
[2122] GGGGG+++G+G++++++GGG++GGGG++++++GGG+GGG+++++GG+++G+aaaa++aaa 3150
pft 177 / 73
[2152] a+a+++++++++++++++++++++++++++aGaGGGGGGGGGGG+++++++++++G+G++ 3152
pft 31 / 177
[2195] ++G++GGGGGGGGG+GGGGGGGGGGGGG+GGGGGGGa+GGGGGGGGGGGGG+GGGGGGGG 3153
pft 38 / 106
[2202] GGGGGGGGGGGGGGGGGGGGGGGGGGGaGGGGGaGGGGGGGGGGGGGGGGGGGGaGGGGG 3153
pft 71 / 82
[2202] GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGaGGGGGGGGGGGGGpriv_ld addRead: 331972
priv_ld total: 383574
Timing BFC paf construct: 383637

ccon timings:
cct pre 1902
cct dir 2814
cct xcu 13785
cct tmp 1411
cct sw 213988
cct pic 1229
cct ico 76207
cct icm 0
cct upd 1430
cct del 0
cct rmz 1369
cct gcp 1260

ccon i timings (2201):
ccit insglcc 77
-------------- Contig statistics ----------------
Contig id: 3400
Contig length: 230

Sanger 454 IonTor PcBioHQ PcBioLQ
Text Solexa Solid
Num. reads 0 0 22 0 0
0 0 0
100% merged reads - - - - -
- 0 0
Max. coverage 0 0 22 0 0
0 0 0
Avg. coverage 0.000 0.000 17.557 0.000 0.000
0.000 0.000 0.000

Max. contig coverage: 22
Avg. contig coverage: 17.557

Consensus contains: A: 54 C: 74 G: 65 T: 37 N: 0
IUPAC: 0 Funny: 0 *: 0
GC content: 60.435%

Contig positions with coverage: 0
-------------------------------------------------
Timing BFC cout constats: 1241
Localtime: Mon Jun 15 19:40:54 2015
bfc 10/0
Marking tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
P 5, marked 0 reads.
Timing BFC edit tricky1: 226
Marking possibly misassembled repeats: [0%] ....|.... [10%] ....|.... [20%]
....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%]
....|.... [80%] ....|.... [90%] ....|.... [100%] done step 1, starting step
2:done. Found none.
Timing BFC mark reps: 292
bfc 11/0
Editing tricky overcalls (SRMs allowed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 0 reads.
Timing BFC edit tricky2: 1588

Searching for single discr. without HAF tags:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Edited 0 positions.
Timing BFC edit single discrepancy, no HAF: 1583
bfc 12/0
Timing BFC delPSHP: 1
bfc 13/0
bfc 14/0
bfc 15/0
bfc 16/0
Transfering reads to readpool.
Timing BFC rp transfer: 72
Done.
bfc 17/0
Looking for best SRM free range in contig
Full contig OK.
returning ret: 0 230
1st covnum: CINFO: 1 22 17.6 20.0 5.7

2nd covnum: CINFO: 1 22 18.5 21.0 4.3

Using: 21
Coverageremove: 0
I have newreptmarked 0 wasmajorovercalledited 0 contignotok 0 continueiter: 0
Timing BFC unused: 980
CUnused: 9
TUnused: 9
AS_used_ids.size(): 1800000
bfc 19
Storing contig ... 10Searching for: SROs UNSs IUPACs, preparing needed data:
sorting tags ... done
makeIntelligentConsensus() complete calc .. mict_fin 8
mict_pre 3
mict_shadow 1
mict_fallout 148
mict_newin 127
mict_helper1 277
mict_newin 127
mict_restofloop 131
mict_totalloop 1158
done.
fetching consensus for strain0 ...done.
Starting search:
done with search
Transfering tags to readpool.
Saving CAF ... done.
Saving MAF ... done.
Saving FASTA ... done.
Saving TCS ... done.
Saving Wiggle ... done.
Saving text ... done.
done.
Timing BFC store con: 2341
Timing BFC loop total: 76589
bfc 1
Localtime: Mon Jun 15 19:40:54 2015

bfc 2
Timing BFC prelim1: 2
bfc 3
bfc 4
Timing BFC discard con: 1
bfc 5
bfc 6/0
bfc 7/0
Building new contig 3401
Localtime: Mon Jun 15 19:40:54 2015
Unused reads: 9
bfc 8/0
0 Known 1: 22
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
[1] +GG++GGGGG+priv_ld addRead: 904
priv_ld total: 990
Timing BFC paf construct: 1020

ccon timings:
cct pre 8
cct dir 7
cct xcu 35
cct tmp 8
cct sw 735
cct pic 2
cct ico 57
cct icm 0
cct upd 1
cct del 0
cct rmz 2
cct gcp 5

ccon i timings (3):
ccit insglcc 0
ccit insglaro 0
ccit insglact 0
ccit insgltot 2
ccit pr 18
ccit templ 3
ccit index 3
ccit biglccins 0
ccit biglinterpol 0
ccit biglupdtags 0
ccit biglfpcri 0
ccit bigllgap 0
ccit biglshiftread 0
ccit bigltot 3
ccit insgr 1
ccit ucv 15

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 4
bfc 9/0
Discarding

Contig does not meet requirement of minimum reads per contig.
Moved 4 reads to debris.
Timing BFC unused: 984
CUnused: 5
TUnused: 5
AS_used_ids.size(): 1800000
bfc 1
Localtime: Mon Jun 15 19:40:54 2015

bfc 2
Timing BFC prelim1: 1
bfc 3
bfc 4
Timing BFC discard con: 0
bfc 5
bfc 6/0
bfc 7/0
Building new contig 3401
Localtime: Mon Jun 15 19:40:54 2015
Unused reads: 5
bfc 8/0
0 Known 1: 4
iter 0, PF init new contig
Known 2: 0
assemblymode_mapping: 0
use general pathfinder: 1
bfccp3
Timing priv_fdns_subFillCache 1 1 1 1 : 1749
Startcache size: 0
Timing priv_fdns_subFillCache 0 0 1 1 : 2068
Startcache size: 0
Timing priv_fdns_subFillCache 0 0 1 1 : 1946
Startcache size: 0
Timing priv_fdns_subFillCache 0 0 0 1 : 1176
Startcache size: 0
Timing priv_fdns_subFillCache 0 0 0 0 : 1325
Startcache size: 1
Timing priv_fdns_genome total: 8292
[1] +GGGpriv_ld addRead: 259
priv_ld total: 281
Timing BFC paf construct: 8605

ccon timings:
cct pre 1
cct dir 2
cct xcu 7
cct tmp 2
cct sw 231
cct pic 0
cct ico 0
cct icm 0
cct upd 0
cct del 0
cct rmz 0
cct gcp 2

ccon i timings (0):
ccit insglcc 0
ccit insglaro 0
ccit insglact 0
ccit insgltot 0
ccit pr 0
ccit templ 0
ccit index 0
ccit biglccins 0
ccit biglinterpol 0
ccit biglupdtags 0
ccit biglfpcri 0
ccit bigllgap 0
ccit biglshiftread 0
ccit bigltot 0
ccit insgr 0
ccit ucv 0

ccon d timings (0):
ccdt ubl 0
ccdt ucv 0
ccdt itf 0
ccdt itb 0
ccdt ccef 0
ccdt cceb 0
ccdt sdt 0
ccdt sr 0
ccdt smp 0
ccdt dt 0
ccdt rr 0
ccdt dsoc 0
ccdt total 0
0 Known 3: 1
Triggering additional cluster check: shouldmovesmallclusterstodebris
startCacheRanDry
Moving small clusters to debris:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done. 4 reads moved to debris.
bfc 9/0
Discarding

Contig does not meet requirement of minimum reads per contig.
Moved 1 reads to debris.
Timing BFC unused: 981
CUnused: 0
TUnused: 0
AS_used_ids.size(): 1800000
Timing BFC unused: 983
CUnused: 0
TUnused: 0
AS_used_ids.size(): 1800000
Saving debris list to file:
SSTrandom_assembly/SSTrandom_d_info/SSTrandom_info_debrislist.txt

Buildstats - RM positions : 19 5
Buildstats - overcall edits : 5426 1989
Buildstats - hash edits : 28536 1774
Buildstats - contig disassemblies: 6 3

ATG PREDICTIONS
-------- CRITICAL warning --------

MIRA warncode: CONCOV_SUSPICIOUS_DISTRIBUTION
Title: Suspicious distribution of contig coverages

- 459 contig(s) with a total of 883921 bases (= 30.1563% of bases in all
non-repetitive large contigs) have an average coverage less than 75% of the
average coverage of all non-repetitive large contigs.
- 233 contig(s) with a total of 492320 bases (= 16.7963% of bases in all
non-repetitive contigs) have an average coverage more than 125% of the average
coverage of all non-repetitive large contigs.
- 692 contig(s) with a total of 1376241 bases (= 46.9526% of bases in all
non-repetitive contigs) have an average coverage 25% above or below the
average coverage of all non-repetitive large contigs.
Summary: found 3 indicator(s) for coverage problem(s).

If the DNA you are assembling is bacterial, this could indicate that you sampled
and sequenced DNA from exponential or late exponential phase of a bacterial
population. This leads to a coverage bias toward the origin of replication,
hence false positive detection of repeats, hence an assembly which is more
fragmented than it could be or may have misassemblies in regions located toward
the opposite of the origin of replication.
Only available countermeasure: for your next sequencing project, do not sample
in exponential phase but sample in stationary phase (if possible).

Performing snapshot 6
Localtime: Mon Jun 15 19:40:54 2015
Creating directory SSTrandom_assembly/SSTrandom_d_chkpt ... done.
Localtime: Mon Jun 15 19:41:09 2015




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

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 32890056 kB
MemFree: 846884 kB
Buffers: 9964 kB
Cached: 18092340 kB
SwapCached: 1360 kB
Active: 20496996 kB
Inactive: 10625180 kB
Active(anon): 11578864 kB
Inactive(anon): 1467016 kB
Active(file): 8918132 kB
Inactive(file): 9158164 kB
Unevictable: 32 kB
Mlocked: 32 kB
SwapTotal: 31249404 kB
SwapFree: 31191288 kB
Dirty: 856392 kB
Writeback: 0 kB
AnonPages: 13018724 kB
Mapped: 128544 kB
Shmem: 26048 kB
Slab: 600220 kB
SReclaimable: 557908 kB
SUnreclaim: 42312 kB
KernelStack: 4824 kB
PageTables: 68412 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 47694432 kB
Committed_AS: 17133260 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 188108 kB
VmallocChunk: 34359513768 kB
HardwareCorrupted: 0 kB
AnonHugePages: 10711040 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 63968 kB
DirectMap2M: 3022848 kB
DirectMap1G: 30408704 kB
--------------------------------------------------------------------------------

Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 5870
Ngid: 0
Pid: 5870
PPid: 5869
TracerPid: 0
Uid: 1000 1000 1000 1000
Gid: 1000 1000 1000 1000
FDSize: 64
Groups: 4 24 27 30 46 108 124 1000
VmPeak: 12801784 kB
VmSize: 12539624 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 12323944 kB
VmRSS: 12323544 kB
VmData: 12526556 kB
VmStk: 184 kB
VmExe: 5792 kB
VmLib: 0 kB
VmPTE: 24108 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/256785
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: 0000001fffffffff
Seccomp: 0
Cpus_allowed: ff
Cpus_allowed_list: 0-7
Mems_allowed: 00000000,00000001
Mems_allowed_list: 0
voluntary_ctxt_switches: 47456
nonvoluntary_ctxt_switches: 1293582
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 1800000 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 184 (184 B)

Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 1800000 7 MiB 0 B 0 B
AS_skim_edges: 0 4.6 GiB 4.6 GiB 0 B
AS_adsfacts: 22012623 481 MiB 61 MiB 0 B
AS_confirmed_edges: 44025244 962 MiB 122 MiB 4 B
AS_permanent_overlap_bans: 1 24 B 0 B 0 B
AS_readhitmiss: 0 24 B 0 B 0 B
AS_readhmcovered: 0 24 B 0 B 0 B
AS_count_rhm: 0 24 B 0 B 0 B
AS_clipleft: 1800000 7 MiB 0 B 0 B
AS_clipright: 1800000 7 MiB 0 B 0 B
AS_used_ids: 0 2 MiB 2 MiB 0 B
AS_multicopies: 1800000 2 MiB 0 B 0 B
AS_hasmcoverlaps: 0 2 MiB 2 MiB 0 B
AS_maxcoveragereached: 1800000 7 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 1800000 2 MiB 0 B 0 B
AS_isdebris: 1800000 2 MiB 0 B 0 B
AS_needalloverlaps: 1800000 2 MiB 0 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 24 B 0 B 0 B
AS_probablermbsnotok: 0 24 B 0 B 0 B
AS_weakrmbsnotok: 0 24 B 0 B 0 B
AS_readmaytakeskim: 0 40 B 0 B 0 B
AS_skimstaken: 0 40 B 0 B 0 B
AS_numskimoverlaps: 0 24 B 0 B 0 B
AS_numleftextendskims: 0 24 B 0 B 0 B
AS_rightextendskims: 0 24 B 0 B 0 B
AS_skimleftextendratio: 0 24 B 0 B 0 B
AS_skimrightextendratio: 0 24 B 0 B 0 B
AS_usedtmpfiles: 69 2 KiB 0 B 0 B
Total: 6529154344 (6.1 GiB)

================================================================================
Dynamic s allocs: 62
Dynamic m allocs: 0
Align allocs: 62


End of assembly process, thank you for using MIRA.
Looking for files named in data ...Pushing back filename:
"/home/user/Desktop/SST/random.fastq"
Starting extraction of large contigs now (this may take a while, please be
patient).

Done.


We're done here, thank you for using MIRA.

• Follow-Ups:
  • [mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures
    • From: Andrej Benjak
  • [mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures
    • From: Chris Hoefler

Other related posts:

• » [mira_talk] Need suggestion on quality of NGS data and post assembly procedures - Rameez Mj
• » [mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures- Andrej Benjak
• » [mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures- Rameez Mj
• » [mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures- Andrej Benjak
• » [mira_talk] Re: Need suggestion on quality of NGS data and post assembly procedures- Chris Hoefler