Hi, I am trying to assemble a genome with pacbio reads. My reads are uncorrected. and I have in total 28245 reads. GC content ~35%, read length mostly 1000-3000. Mira ran for about half an hour before it crashed. And I have included the output from mira and my manifest file. Thank you very much for your help! Best wishes, Chenling
$ mira yakuba.manifest
This is MIRA 4.0.2_0+g29f87d4 .
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 14:57:56 CEST 2014
On: Darwin airfau2.fritz.box 13.1.0 Darwin Kernel Version 13.1.0: Thu Jan 16
19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64 x86_64
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: Darwin oem-rvjt7sua9kt 13.1.0 Darwin Kernel Version 13.1.0: Thu
Jan 16 19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64 x86_64
Looking for files named in data ...Pushing back filename:
"/Users/Chenling/TurelliLab/pacbio/line08/all.mapped.fastq"
Manifest:
projectname: Yakuba
job: genome,denovo,accurate
parameters: -GE:not=4 -NW:cmrnl=no -SK:bph=10 -SK:hss=2 -SK:not=8
Manifest load entries: 1
MLE 1:
RGID: 1
RGN: pacbio_kevin SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 4 (PcBioLQ) namschem: 6 SID: 0
DQ: 5
BB: 0 Rail: 0 CER: 0
/Users/Chenling/TurelliLab/pacbio/line08/all.mapped.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 : Yakuba
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) : [pbl] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 4
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 2
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [pbl] 100
Minimum reads per contig (mrpc) : [pbl] 2
Enforce presence of qualities (epoq) : [pbl] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [pbl] 2
Minimum length (ardml) : [pbl] 200
Grace length (ardgl) : [pbl] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [pbl] 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) : [pbl] no
Read extension window length (rewl) : [pbl] 15
Read extension w. maxerrors (rewme) : [pbl] 2
First extension in pass (feip) : [pbl] 0
Last extension in pass (leip) : [pbl] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [pbl] 10
Max front gap (msvsmfg) : [pbl] 60
Max end gap (msvsmeg) : [pbl] 120
Strict front clip (msvssfc) : [pbl] 0
Strict end clip (msvssec) : [pbl] 0
Possible vector leftover clip (pvlc) : [pbl] no
maximum len allowed (pvcmla) : [pbl] 18
Min qual. threshold for entire read (mqtfer): [pbl] 0
Number of bases (mqtfernob) : [pbl] 0
Quality clip (qc) : [pbl] no
Minimum quality (qcmq) : [pbl] 20
Window length (qcwl) : [pbl] 30
Bad stretch quality clip (bsqc) : [pbl] no
Minimum quality (bsqcmq) : [pbl] 5
Window length (bsqcwl) : [pbl] 20
Masked bases clip (mbc) : [pbl] no
Gap size (mbcgs) : [pbl] 20
Max front gap (mbcmfg) : [pbl] 40
Max end gap (mbcmeg) : [pbl] 60
Lower case clip front (lccf) : [pbl] no
Lower case clip back (lccb) : [pbl] no
Clip poly A/T at ends (cpat) : [pbl] no
Keep poly-a signal (cpkps) : [pbl] no
Minimum signal length (cpmsl) : [pbl] 12
Max errors allowed (cpmea) : [pbl] 1
Max gap from ends (cpmgfe) : [pbl] 9
Clip 3 prime polybase (c3pp) : [pbl] no
Minimum signal length (c3ppmsl) : [pbl] 15
Max errors allowed (c3ppmea) : [pbl] 3
Max gap from ends (c3ppmgfe) : [pbl] 9
Clip known adaptors right (ckar) : [pbl] no
Ensure minimum left clip (emlc) : [pbl] no
Minimum left clip req. (mlcr) : [pbl] 25
Set minimum left clip to (smlc) : [pbl] 30
Ensure minimum right clip (emrc) : [pbl] no
Minimum right clip req. (mrcr) : [pbl] 10
Set minimum right clip to (smrc) : [pbl] 20
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : [pbl] no
Bases per hash (pecbph) : 17
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [pbl] 1
Back freq (pbfreq) : [pbl] 1
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [pbl] no
Back forward-rev (pbfore) : [pbl] no
Front conf. multi-seq type (pfcmst) : [pbl] no
Back conf. multi-seq type (pbcmst) : [pbl] no
Front seen at low pos (pfsalp) : [pbl] no
Back seen at low pos (pbsalp) : [pbl] no
Clip bad solexa ends (cbse) : [pbl] no
Search PhiX174 (spx174) : [pbl] no
Filter PhiX174 (fpx174) : [pbl] no
Rare kmer mask (rkm) : [pbl] 0
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 8
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 10
Automatic increase per pass (bphaipp) : 1
Automatic incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 2
Percent required (pr) : [pbl] 80
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 90
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) : [pbl] yes
Quick rule min len 1 (qrml1) : [pbl] 80
Quick rule min sim 1 (qrms1) : [pbl] 90
Quick rule min len 2 (qrml2) : [pbl] 60
Quick rule min sim 2 (qrms2) : [pbl] 95
Backbone quick overlap min len (bqoml) : [pbl] 80
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [pbl] 50
Bandwidth max (bmax) : [pbl] 1000
Bandwidth min (bmin) : [pbl] 25
Minimum score (ms) : [pbl] 150
Minimum overlap (mo) : [pbl] 17
Minimum relative score in % (mrs) : [pbl] 10
Solexa_hack_max_errors (shme) : [pbl] -1
Extra gap penalty (egp) : [pbl] no
extra gap penalty level (egpl) : [pbl] low
Max. egp in percent (megpp) : [pbl] 100
Contig parameters (-CO):
Name prefix (np) : Yakuba
Reject on drop in relative alignment score in % (rodirs) : [pbl] 30
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [pbl] 6
Minimum neighbour quality needed for tagging (mnq) : [pbl] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [pbl] 25
End-read Marking Exclusion Area in bases (emea) : [pbl] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [pbl] no
Also mark gap bases - even multicolumn (amgbemc) : [pbl] yes
Also mark gap bases - need both strands (amgbnbs): [pbl] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [pbl] no
Merge short reads (msr) : [pbl] no
Max errors (msrme) : [pbl] 0
Keep ends unmerged (msrkeu) : [pbl] -1
Gap override ratio (gor) : [pbl] 66
Edit options (-ED):
Mira automatic contig editing (mace) : no
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [pbl] no
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) : no
Max read name length (mrnl) : 40
Check average coverage (cac) : stop
Average coverage value (acv) : 80
Directories (-DI):
Top directory for writing files : Yakuba_assembly
For writing result files : Yakuba_assembly/Yakuba_d_results
For writing result info files : Yakuba_assembly/Yakuba_d_info
For writing tmp files : Yakuba_assembly/Yakuba_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : Yakuba_assembly/Yakuba_d_chkpt
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [pbl] no
Save tagged singlets in project (stsip) : [pbl] 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 : Yakuba_out.caf
MAF : Yakuba_out.maf
FASTA : Yakuba_out.unpadded.fasta
FASTA quality : Yakuba_out.unpadded.fasta.qual
FASTA (padded) : Yakuba_out.padded.fasta
FASTA qual.(pad): Yakuba_out.padded.fasta.qual
GAP4 (directory): Yakuba_out.gap4da
ACE : Yakuba_out.ace
HTML : Yakuba_out.html
Simple text : Yakuba_out.txt
TCS overview : Yakuba_out.tcs
Wiggle : Yakuba_out.wig
------------------------------------------------------------------------------
Deleting old directory Yakuba_assembly ... done.
Creating directory Yakuba_assembly ... done.
Creating directory Yakuba_assembly/Yakuba_d_results ... done.
Creating directory Yakuba_assembly/Yakuba_d_info ... done.
Creating directory Yakuba_assembly/Yakuba_d_chkpt ... done.
Creating directory Yakuba_assembly/Yakuba_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Wed May 14 13:34:24 2014
Loading reads from /Users/Chenling/TurelliLab/pacbio/line08/all.mapped.fastq
type fastq
Localtime: Wed May 14 13:34:24 2014
Loading data from FASTQ file:
/Users/Chenling/TurelliLab/pacbio/line08/all.mapped.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 28245 reads, Localtime: Wed May 14 13:34:24 2014
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
List of read names which have problems with name length:
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/580/10501_14036
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/580/14085_16055
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/741/2633_6925
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/741/6975_10522
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/1017/0_6772
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/1017/6817_9723
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/1689/0_437
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/1689/486_993
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/1902/0_6893
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3081/0_3502
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3245/3388_5539
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3245/5593_8257
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3245/8305_10694
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3245/10744_12875
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3245/12925_15093
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3245/15139_16149
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3412/0_2833
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3412/2881_7694
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3412/7736_12011
Name too long:
m130809_071715_42198_c100563952550000001823088712221382_s1_p0/3511/2877_8088
28245 reads had a long name length, for brevity's sake not all were listed.
WARNING!
-------- MINOR warning --------
MIRA warncode: READ_NAME_TOO_LONG
Title: Long read names
28245 reads were detected with names longer than 40 characters (see output log
for more details).
While MIRA and many other programs have no problem with that, some older
programs have restrictions concerning the length of the read name.
Example given: the pipeline
CAF -> caf2gap -> gap2caf
will stop working at the gap2caf stage if there are read names having > 40
characters where the names differ only at >40 characters.
This is a warning only, but as a couple of people were bitten by this, the
default behaviour of MIRA is to stop when it sees that potential problem.
You might want to rename your reads to have <= 40 characters. Instead of
renaming reads in the input files, maybe the 'rename_prefix' functionality of
manifest files is useful for you there.
On the other hand, you also can ignore this potential problem and force MIRA to
continue by using the parameter: '-NW:cmrnl=warn' or '-NW:cmrnl=no'
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.
28245 reads with valid data for assembly.
Localtime: Wed May 14 13:34:24 2014
Generated 28245 unique DNA template ids for 28245 valid reads.
No useful template information found.
TODO: Like Readpool: strain x has y reads
Have read pool with 28245 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 28245 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 28090 0 0 0
Avg tot rlen 0 0 0 0 2207 0 0 0
Avg rlen used 0 0 0 0 2218 0 0 0
W/o clips 0 0 0 0 28245 0 0 0
PcBioLQ total bases: 62341436 used bases in used reads: 62329400
===========================================================================
Checking pairs of readgroup 1 (named: 'pacbio_kevin'): found 0
Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_clippings_t0.0.txt
Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_clippings_t1.0.txt
Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_clippings_t2.0.txt
Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_clippings_t3.0.txt
Post-load clips:
Localtime: Wed May 14 13:34:25 2014
Writing temporary hstat files:
freemem: 10945101824
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: Wed May 14 13:34:25 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Wed May 14 13:34:25 2014
clean up temporary stat files...Localtime: Wed May 14 13:34:25 2014
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Wed May 14 13:34:25 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 28245 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 28090 0 0 0
Avg tot rlen 0 0 0 0 2207 0 0 0
Avg rlen used 0 0 0 0 2218 0 0 0
W/o clips 0 0 0 0 28245 0 0 0
PcBioLQ total bases: 62341436 used bases in used reads: 62329400
===========================================================================
Sorting reads ... done.
Tmp directory is not on a NFS mount, good.
PRED MAXTID 28244
No bases clipped in first pec round, skipping second round.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 28245 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 28090 0 0 0
Avg tot rlen 0 0 0 0 2207 0 0 0
Avg rlen used 0 0 0 0 2218 0 0 0
W/o clips 0 0 0 0 28245 0 0 0
PcBioLQ total bases: 62341436 used bases in used reads: 62329400
===========================================================================
Performing snapshot 1
Localtime: Wed May 14 13:34:26 2014
Creating directory Yakuba_assembly/Yakuba_d_chkpt ... done.
Localtime: Wed May 14 13:34:28 2014
Could not read file /proc/self/status
--------------------------------------------------------------------------------
Pass: 1 / 4
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 28245 0 0 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 28090 0 0 0
Avg tot rlen 0 0 0 0 2207 0 0 0
Avg rlen used 0 0 0 0 2218 0 0 0
W/o clips 0 0 0 0 28245 0 0 0
PcBioLQ total bases: 62341436 used bases in used reads: 62329400
===========================================================================
Localtime: Wed May 14 13:34:28 2014
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: Wed May 14 13:34:55 2014
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Wed May 14 13:34:55 2014
clean up temporary stat files...Localtime: Wed May 14 13:34:55 2014
Raw MHI: 798364
Raw avg. freq. : 145
HSS 1048405 HSST: 943565
Localtime: Wed May 14 13:34:55 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 145
Corrected avg. raw frequency coverage: 145
Final average frequency: 145
Deduced thresholds:
-------------------
Min normal cov: 58
Max normal cov: 232
Repeat cov: 275.5
Heavy cov: 1160
Crazy cov: 2900
Mask cov: 14500
Repeat ratio histogram:
-----------------------
0 551718
1 353474
2 84130
3 29679
4 13404
5 6342
6 3205
7 1951
8 1409
9 927
10 578
11 390
12 246
13 195
14 162
15 127
16 97
17 70
18 58
19 28
20 36
21 32
22 21
23 12
24 4
25 8
26 4
27 4
28 6
29 8
31 8
32 4
33 4
34 1
35 4
36 4
37 10
38 6
39 10
41 2
42 2
43 3
45 2
47 2
49 2
52 2
54 2
56 2
57 2
60 2
68 2
76 2
663 2
=========================================================
Assigning statistics values:
Localtime: Wed May 14 13:34:55 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] Localtime: Wed May 14 13:34:57 2014
Buntifying reads ... done.
Adding fork tags ... done.
Writing read repeat info to:
Yakuba_assembly/Yakuba_d_info/Yakuba_info_readrepeats.lst ... 0 sequences with
0 masked stretches.
AS_resumeasembly 0
AS_resumeisok 0
fileExists(Yakuba_assembly/Yakuba_d_tmp/Yakuba_signal_findpossibleoverlaps_pass.1.ok)
0
Localtime: Wed May 14 13:34:59 2014
Searching for possible overlaps:
WARNING!!!!!!
You are not performing a 'mapping only' assembly and the parameters
-SK:bph=10 and -SK:hss=2
are quite low. If SKIM takes ages, stop this assembly and restart while
increasing these parameters.
Localtime: Wed May 14 13:34:59 2014
Now running threaded and partitioned skimmer with 3 partitions in 8 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
truncating Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_posmatchf_pass.1.bin
truncated Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_posmatchf_pass.1.bin from
8310336 to 7001328
truncating Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_posmatchc_pass.1.bin
truncated Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_posmatchc_pass.1.bin from
8061744 to 6774624
Hits chosen: 1147996
Localtime: Wed May 14 13:39:41 2014
Total megahubs: 1
MIRA has detected megahubs in your data.This may not be a problem, but most
probably is, especially for eukaryotes.
Cutting back possible chimeras ... done.
Chimeras were searched for ... looking for hits to purge.
truncating Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_posmatchf_pass.1.bin from
7001328 to 7001328
truncating Yakuba_assembly/Yakuba_d_tmp/Yakuba_int_posmatchc_pass.1.bin from
6774624 to 6774624
System memory: 62087168
Mem2keepfree: 9313075
Used by MIRA: 0
Mem avail: 52774093
rsh not increased.
Edge vector capacity: 1210395
Can load up to 1205395 skim edges at once.
Partitioning into 1 blocks.
Blocks: 28245
We have 1147996 skims in file.
Localtime: Wed May 14 13:39:41 2014
De-normalising SKIM hits ... (this will take a while)
Localtime: Wed May 14 13:39:41 2014
Localtime: Wed May 14 13:39:41 2014
Writing normalised skimblock 0 ( 35 MiB) ... done.
Localtime: Wed May 14 13:39:41 2014
Loading block 0
Only one block, already loaded.
Localtime: Wed May 14 13:39:41 2014
Step 0
Loading block 0
Only one block, already loaded.
Localtime: Wed May 14 13:39:41 2014
Only long reads
Step 10
Loading block 0
Only one block, already loaded.
Total skims taken: 29104
Step 20
Loading block 0
Only one block, already loaded.
Total skims taken: 29104
Step 30
Loading block 0
Only one block, already loaded.
Total skims taken: 166853
Step 40
Loading block 0
Only one block, already loaded.
Total skims taken: 166853
Step 50
Total skims taken: 166853
Step 53
Loading block 0
Only one block, already loaded.
Total skims taken: 176420
Step 55
Loading block 0
Only one block, already loaded.
Total skims taken: 179666
Step 60
Loading block 0
Only one block, already loaded.
Total skims taken: 179953
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: 179953
Filtering forward skims.
Localtime: Wed May 14 13:39:41 2014
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done.
Filtering complement skims.
Localtime: Wed May 14 13:39:41 2014
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Done all filtering.
Localtime: Wed May 14 13:39:42 2014
Making alignments.
Localtime: Wed May 14 13:39:42 2014
Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.Failure, wrapped MIRA process aborted.Attachment:
yakuba.manifest
Description: Binary data
