[mira_talk] Re: results folder empty
- From: Tarah Lynch <tarah.lynch@xxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 10 May 2011 12:13:32 -0500
Yes - a little annoying, however I am new to this, so I was expecting
glitches :) We are using 3.2.1.11.
I actually tried doing another assembly and accidentally wrote over the
log_assembly file, however my second attempt also ended early and I have
attached it.
Are there any other files from the first project that would be helpful for
figuring out why it didn't work as the info files were different so I'm
guessing the errors are different too?
Thank you,
Tarah
From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Date: 2011-05-10 10:35 AM
Subject: [mira_talk] Re: results folder empty
Sent by: mira_talk-bounce@xxxxxxxxxxxxx
How annoying. I suppose you used 3.2.1? Can you please send the output
log? (log_assembly.txt or whatever you named it)
B.
----- original message --------
Subject: [mira_talk] results folder empty
Sent: Mon, 09 May 2011
From: Tarah Lynch
Hello,
I just ran an assembly on a bacterial genome using solexa and 454 data -
MIRA ran for 5-6 days. The info file looks like we should have some
contigs to work with etc. but the results file is completely empty :(
Help please.
Tarah
--- original message end ----
This is MIRA V3.2.1.11 (development version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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 new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.
Compiled by: bach
Fri Mar 25 19:48:06 CET 2011
On: Linux arcadia 2.6.35-28-generic #49-Ubuntu SMP Tue Mar 1 14:39:03 UTC 2011
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 lightning.corefacility.ca 2.6.18-194.32.1.el5 #1 SMP Wed
Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=stable --job=denovo,genome,accurate,454,solexa
-GE:not=24 454_SETTINGS -AS:mrl=80 SOLEXA_SETTINGS -AS:mrl=80:mrpc=15
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), 454 data, Solexa data
Used parameter settings:
General (-GE):
Project name in (proin) : stable
Project name out (proout) : stable
Number of threads (not) : 24
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[454] yes
[sxa] yes
Template insert size minimum (tismin) : [san] -1
[454] -1
[sxa] -1
Template insert size maximum (tismax) : [san] -1
[454] -1
[sxa] -1
Template partner build direction (tpbd) : [san] -1
[454] -1
[sxa] -1
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] no
[454] yes
[sxa] yes
File type (ft) : [san] fasta
[454] fasta
[sxa] fastq
External quality (eq) : from SCF (scf)
Ext. qual. override (eqo) : no
Discard reads on e.q. error (droeqe): no
Solexa scores in qual file (ssiqf) : no
FASTQ qual offset (fqqo) : [san] 0
[454] 0
[sxa] 0
Wants quality file (wqf) : [san] yes
[454] yes
[sxa] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[454] forward/reverse
(fr)
[sxa] Solexa (solexa)
Merge with XML trace info (mxti) : [san] no
[454] yes
[sxa] no
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 5
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 3
Minimum read length (mrl) : [san] 80
[454] 80
[sxa] 80
Minimum reads per contig (mrpc) : [san] 2
[454] 5
[sxa] 15
Base default quality (bdq) : [san] 10
[454] 10
[sxa] 10
Enforce presence of qualities (epoq) : [san] yes
[454] yes
[sxa] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[454] 2
[sxa] 2.5
Minimum length (ardml) : [san] 400
[454] 200
[sxa] 300
Grace length (ardgl) : [san] 40
[454] 20
[sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [san] 1.5
[454] 1.5
[sxa] 1.5
Keep long repeats separated (klrs) : no
Spoiler detection (sd) : yes
Last pass only (sdlpo) : yes
Use genomic pathfinder (ugpf) : yes
Use emergency search stop (uess) : yes
ESS partner depth (esspd) : 500
Use emergency blacklist (uebl) : yes
Use max. contig build time (umcbt) : no
Build time in seconds (bts) : 10000
Strain and backbone options (-SB):
Load straindata (lsd) : no
Assign default strain (ads) : [san] no
[454] no
[sxa] no
Default strain name (dsn) : [san] StrainX
[454] StrainX
[sxa] StrainX
Load backbone (lb) : no
Start backbone usage in pass (sbuip) : 3
Backbone file type (bft) : fasta
Backbone base quality (bbq) : 30
Backbone strain name (bsn) : ReferenceStrain
Force for all (bsnffa) : no
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Also build new contigs (abnc) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [san] yes
[454] no
[sxa] no
Read extension window length (rewl) : [san] 30
[454] 15
[sxa] 30
Read extension w. maxerrors (rewme) : [san] 2
[454] 2
[sxa] 2
First extension in pass (feip) : [san] 0
[454] 0
[sxa] 0
Last extension in pass (leip) : [san] 0
[454] 0
[sxa] 0
Clipping options (-CL):
Merge with SSAHA2/SMALT vector screen (msvs): [san] no
[454] no
[sxa] no
Gap size (msvsgs) : [san] 10
[454] 8
[sxa] 1
Max front gap (msvsmfg) : [san] 60
[454] 8
[sxa] 2
Max end gap (msvsmeg) : [san] 120
[454] 12
[sxa] 2
Strict front clip (msvssfc) : [san] 0
[454] 0
[sxa] 0
Strict end clip (msvssec) : [san] 0
[454] 0
[sxa] 0
Possible vector leftover clip (pvlc) : [san] yes
[454] no
[sxa] no
maximum len allowed (pvcmla) : [san] 18
[454] 18
[sxa] 18
Min qual. threshold for entire read (mqtfer): [san] 0
[454] 0
[sxa] 5
Number of bases (mqtfernob) : [san] 0
[454] 0
[sxa] 15
Quality clip (qc) : [san] no
[454] no
[sxa] no
Minimum quality (qcmq) : [san] 20
[454] 20
[sxa] 20
Window length (qcwl) : [san] 30
[454] 30
[sxa] 30
Bad stretch quality clip (bsqc) : [san] yes
[454] no
[sxa] no
Minimum quality (bsqcmq) : [san] 20
[454] 5
[sxa] 5
Window length (bsqcwl) : [san] 30
[454] 20
[sxa] 20
Masked bases clip (mbc) : [san] yes
[454] yes
[sxa] no
Gap size (mbcgs) : [san] 20
[454] 5
[sxa] 5
Max front gap (mbcmfg) : [san] 40
[454] 12
[sxa] 12
Max end gap (mbcmeg) : [san] 60
[454] 12
[sxa] 12
Lower case clip (lcc) : [san] no
[454] yes
[sxa] no
Clip poly A/T at ends (cpat) : [san] no
[454] no
[sxa] no
Keep poly-a signal (cpkps) : [san] no
[454] no
[sxa] no
Minimum signal length (cpmsl) : [san] 12
[454] 12
[sxa] 12
Max errors allowed (cpmea) : [san] 1
[454] 1
[sxa] 1
Max gap from ends (cpmgfe) : [san] 9
[454] 9
[sxa] 9
Clip 3 prime polybase (c3pp) : [san] no
[454] no
[sxa] yes
Minimum signal length (c3ppmsl) : [san] 12
[454] 12
[sxa] 12
Max errors allowed (c3ppmea) : [san] 2
[454] 2
[sxa] 2
Max gap from ends (c3ppmgfe) : [san] 9
[454] 9
[sxa] 9
Ensure minimum left clip (emlc) : [san] yes
[454] no
[sxa] no
Minimum left clip req. (mlcr) : [san] 25
[454] 4
[sxa] 0
Set minimum left clip to (smlc) : [san] 30
[454] 4
[sxa] 0
Ensure minimum right clip (emrc) : [san] no
[454] no
[sxa] no
Minimum right clip req. (mrcr) : [san] 10
[454] 10
[sxa] 10
Set minimum right clip to (smrc) : [san] 20
[454] 15
[sxa] 20
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : yes
Bases per hash (pecbph) : 27
Handle Solexa GGCxG problem (pechsgp) : yes
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 24
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 19
Hash save stepping (hss) : 1
Percent required (pr) : [san] 85
[454] 85
[sxa] 90
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0
Freq. est. min normal (fenn) : 0.4
Freq. est. max normal (fexn) : 1.6
Freq. est. repeat (fer) : 1.9
Freq. est. heavy repeat (fehr) : 8
Freq. est. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Repeat level in info file (rliif) : 6
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 4096
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[454] yes
[sxa] yes
Quick rule min len 1 (qrml1) : [san] 200
[454] 80
[sxa] 33
Quick rule min sim 1 (qrms1) : [san] 90
[454] 90
[sxa] 100
Quick rule min len 2 (qrml2) : [san] 100
[454] 60
[sxa] 30
Quick rule min sim 2 (qrms2) : [san] 95
[454] 95
[sxa] 100
Backbone quick overlap min len (bqoml) : [san] 150
[454] 80
[sxa] 20
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[454] 20
[sxa] 20
Bandwidth max (bmax) : [san] 130
[454] 80
[sxa] 80
Bandwidth min (bmin) : [san] 25
[454] 20
[sxa] 20
Minimum score (ms) : [san] 30
[454] 15
[sxa] 15
Minimum overlap (mo) : [san] 15
[454] 20
[sxa] 25
Minimum relative score in % (mrs) : [san] 70
[454] 70
[sxa] 90
Solexa_hack_max_errors (shme) : [san] 0
[454] 0
[sxa] 0
Extra gap penalty (egp) : [san] no
[454] yes
[sxa] no
extra gap penalty level (egpl) : [san] low
[454] reject_codongaps
[sxa] low
Max. egp in percent (megpp) : [san] 100
[454] 100
[sxa] 100
Contig parameters (-CO):
Name prefix (np) : stable
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[454] 30
[sxa] 30
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[454] 4
[sxa] 4
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[454] 20
[sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[454] 25
[sxa] 30
End-read Marking Exclusion Area in bases (emea) : [san] 1
[454] 1
[sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[454] no
[sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[454] yes
[sxa] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[454] yes
[sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[454] no
[sxa] no
Merge short reads (msr) : [san] no
[454] no
[sxa] no
Gap override ratio (gor) : [san] 66
[454] 66
[sxa] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[454] yes
[sxa] no
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Misc (-MI):
Stop on NFS (sonfs) : yes
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 5000
Directories (-DI):
When loading EXP files :
When loading SCF files :
Top directory for writing files : stable_assembly
For writing result files : stable_assembly/stable_d_results
For writing result info files : stable_assembly/stable_d_info
For writing log files : stable_assembly/stable_d_log
Log redirected to (lrt) :
For writing checkpoint files : stable_assembly/stable_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
stable_in.sanger.fasta
[454]
stable_in.454.fasta
[sxa]
stable_in.solexa.fasta
When loading qualities from FASTA quality : [san]
stable_in.sanger.fasta.qual
[454]
stable_in.454.fasta.qual
[sxa]
stable_in.solexa.fasta.qual
When loading sequences from FASTQ : [san]
stable_in.sanger.fastq
[454]
stable_in.454.fastq
[sxa]
stable_in.solexa.fastq
When loading project from CAF : stable_in.sanger.caf
When loading project from MAF (disabled) : stable_in.sanger.maf
When loading EXP fofn : stable_in.sanger.fofn
When loading project from PHD : stable_in.phd.1
When loading strain data : stable_straindata_in.txt
When loading XML trace info files : [san]
stable_traceinfo_in.sanger.xml
[454]
stable_traceinfo_in.454.xml
[sxa]
stable_traceinfo_in.solexa.xml
When loading SSAHA2 vector screen results :
stable_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
stable_smaltvectorscreen_in.txt
When loading backbone from MAF : stable_backbone_in.maf
When loading backbone from CAF : stable_backbone_in.caf
When loading backbone from GenBank : stable_backbone_in.gbf
When loading backbone from GFF3 : stable_backbone_in.gff3
When loading backbone from FASTA : stable_backbone_in.fasta
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[454] no
[sxa] no
Save tagged singlets in project (stsip) : [san] yes
[454] yes
[sxa] yes
Remove rollover logs (rrol) : yes
Remove log directory (rld) : no
Result files:
Saved as CAF (orc) : yes
Saved as MAF (orm) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : yes
Saved as GFF3 (org3) : no
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : no
Saved as wiggle (orw) : yes
Temporary result files:
Saved as CAF (otc) : yes
Saved as MAF (otm) : no
Saved as FASTA (otf) : no
Saved as GAP4 (directed assembly) (otg) : no
Saved as phrap ACE (ota) : no
Saved as HTML (oth) : no
Saved as Transposed Contig Summary (ots) : no
Saved as simple text format (ott) : no
Extended temporary result files:
Saved as CAF (oetc) : no
Saved as FASTA (oetf) : no
Saved as GAP4 (directed assembly) (oetg) : no
Saved as phrap ACE (oeta) : no
Saved as HTML (oeth) : no
Save also singlets (oetas) : no
Alignment output customisation:
TEXT characters per line (tcpl) : 60
HTML characters per line (hcpl) : 60
TEXT end gap fill character (tegfc) :
HTML end gap fill character (hegfc) :
File / directory output names:
CAF : stable_out.caf
MAF : stable_out.maf
FASTA : stable_out.unpadded.fasta
FASTA quality : stable_out.unpadded.fasta.qual
FASTA (padded) : stable_out.padded.fasta
FASTA qual.(pad): stable_out.padded.fasta.qual
GAP4 (directory): stable_out.gap4da
ACE : stable_out.ace
HTML : stable_out.html
Simple text : stable_out.txt
TCS overview : stable_out.tcs
Wiggle : stable_out.wig
------------------------------------------------------------------------------
Creating directory stable_assembly ... done.
Creating directory stable_assembly/stable_d_log ... done.
Creating directory stable_assembly/stable_d_results ... done.
Creating directory stable_assembly/stable_d_info ... done.
Creating directory stable_assembly/stable_d_chkpt ... done.
Log directory is not on a NFS mount, good.
Localtime: Mon May 9 16:23:52 2011
Loading data (454) from FASTA files,
Localtime: Mon May 9 16:23:52 2011
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Found 291212 sequences.
Localtime: Mon May 9 16:24:04 2011
454 will load 291212 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Mon May 9 16:24:04 2011
Counting sequences in FASTQ file: found 17710678 sequences.
Localtime: Mon May 9 16:24:27 2011
Solexa will load 17710678 reads.
Longest Sanger: 0
Longest 454: 1200
Longest PacBio: 0
Longest Solexa: 97
Longest Solid: 0
Longest overall: 1200
Total reads to load: 18001890
Reserving space for reads (this may take a while)
tcmalloc: large alloc 4176441344 bytes == 0x1e19a000 @
Reserved space for 18001900 reads.
Loading data (454) from FASTA files,
Localtime: Mon May 9 16:24:27 2011
Localtime: Mon May 9 16:24:27 2011
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon May 9 16:24:36 2011
rnm size: 0
Loading quality data from FASTA quality file stable_in.454.fasta.qual:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Localtime: Mon May 9 16:25:21 2011
Done.
Loaded 291212 reads with 174749466 raw bases.
291212 reads have quality accounted for.
Loaded 291212 454 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Mon May 9 16:25:21 2011
Counting sequences in FASTQ file: found 17710678 sequences.
Localtime: Mon May 9 16:25:42 2011
Using calculated FASTQ quality offset: 66
Localtime: Mon May 9 16:25:42 2011
Loading data from FASTQ file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
Done.
Loaded 17710678 reads, Localtime: Mon May 9 16:27:10 2011
Loaded 17710678 Solexa reads.
Total reads loaded: 18001890
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 264278544 kB
MemFree: 74301400 kB
Buffers: 617572 kB
Cached: 169145956 kB
SwapCached: 0 kB
Active: 47223924 kB
Inactive: 139221816 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 264278544 kB
LowFree: 74301400 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 28 kB
Writeback: 0 kB
AnonPages: 16682072 kB
Mapped: 42752 kB
Slab: 3446604 kB
PageTables: 41104 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 132139272 kB
Committed_AS: 17146976 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 263048 kB
VmallocChunk: 34359475119 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 0%
Tgid: 18617
Pid: 18617
PPid: 18555
TracerPid: 0
Uid: 40074 40074 40074 40074
Gid: 40004 40004 40004 40004
FDSize: 256
Groups: 40004
VmPeak: 16758200 kB
VmSize: 16758196 kB
VmLck: 0 kB
VmHWM: 16570880 kB
VmRSS: 16570880 kB
VmData: 16753016 kB
VmStk: 88 kB
VmExe: 5056 kB
VmLib: 0 kB
VmPTE: 32404 kB
StaBrk: 1db98000 kB
Brk: 41c393000 kB
StaStk: 7fffe04cbac0 kB
Threads: 1
SigQ: 0/2105344
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,ffffffff
Mems_allowed: 00000000,00000001
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 18001890 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 13509099488 (12.6 GiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 0 24 B 0 B 0 B
AS_skim_edges: 0 24 B 0 B 0 B
AS_adsfacts: 0 24 B 0 B 0 B
AS_confirmed_edges: 0 24 B 0 B 0 B
AS_permanent_overlap_bans: 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: 0 24 B 0 B 0 B
AS_clipright: 0 24 B 0 B 0 B
AS_used_ids: 0 24 B 0 B 0 B
AS_multicopies: 0 24 B 0 B 0 B
AS_hasmcoverlaps: 0 24 B 0 B 0 B
AS_maxcoveragereached: 0 24 B 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 0 24 B 0 B 0 B
AS_isdebris: 0 24 B 0 B 0 B
AS_needalloverlaps: 0 40 B 0 B 0 B
AS_readsforrepeatresolve: 0 40 B 0 B 0 B
AS_allrmbsok: 0 24 B 0 B 0 B
AS_probablermbsnotok: 0 24 B 0 B 0 B
AS_weakrmbsnotok: 0 24 B 0 B 0 B
AS_readmaytakeskim: 0 40 B 0 B 0 B
AS_skimstaken: 0 40 B 0 B 0 B
AS_numskimoverlaps: 0 24 B 0 B 0 B
AS_numleftextendskims: 0 24 B 0 B 0 B
AS_rightextendskims: 0 24 B 0 B 0 B
AS_skimleftextendratio: 0 24 B 0 B 0 B
AS_skimrightextendratio: 0 24 B 0 B 0 B
AS_usedlogfiles: 1 48 B 0 B 0 B
Total: 13509100296 (12.6 GiB)
================================================================================
Localtime: Mon May 9 16:27:12 2011
Localtime: Mon May 9 16:27:12 2011
Merging data from XML trace info file stable_traceinfo_in.454.xml ...Num reads:
291212
Building hash table ... done.
Localtime: Mon May 9 16:27:54 2011
Generated 9146551 unique template ids for 18001890 valid reads.
Done merging XML data, matched 291212 reads.
Localtime: Mon May 9 16:28:39 2011
Checking reads for trace data:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
No SCF data present in any read, automatic contig editing for Sanger data is
now switched off.
18001890 reads with valid data for assembly.
Localtime: Mon May 9 16:29:22 2011
Generated 9146551 unique template ids for 18001890 valid reads.
Localtime: Mon May 9 16:30:09 2011
Generated 0 unique strain ids for 18001890 reads.
Strain "default" has 18001890 reads.
Have read pool with 18001890 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 0 291212 0 17710678 0
Reads wo qual 0 0 0 0 0
Used reads 0 275260 0 16736536 0
Avg tot rlen 0 600 0 82 0
Avg rlen used 0 359 0 86 0
With strain 0 0 0 0 0
W/o clips 0 3859 0 17710678 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:174749466 used bases in used reads: 98999030
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:1469933809 used bases in used reads: 1442637081
Solid total bases:0 used bases in used reads: 0
===========================================================================
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 PacBio Solexa SOLiD
----------------------------------------
Total reads 0 291212 0 17710678 0
Reads wo qual 0 0 0 0 0
Used reads 0 275260 0 16735881 0
Avg tot rlen 0 600 0 82 0
Avg rlen used 0 359 0 86 0
With strain 0 0 0 0 0
W/o clips 0 3859 0 17710678 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:174749466 used bases in used reads: 98999030
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:1469933809 used bases in used reads: 1442574108
Solid total bases:0 used bases in used reads: 0
===========================================================================
Starting Solexa adaptor right clip ... Localtime: Mon May 9 16:30:58 2011
Searching multithread now ...
24
Searching for Solexa partial end adaptors ...
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done. Clipped 383 reads.
Starting minimum quality threshold clip ... done. Killed 771096 reads.
Starting clips: d
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