[mira_talk] Error while loading adsfacts during denovo assembly
- From: Surya Saha <ss2489@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 26 Aug 2011 09:41:17 -0400
Hi Everybody,
I am running a denovo assembly of a bacterial genome having ~150X coverage
(sampled from 2000X+ coverage dataset) and 7 million Illumina paired end
100bp reads on a 64GB RAM machine using MIRA 3.4.0. Here are my parameters
mira --project=9gb_28e6_def --job=denovo,genome,accurate,solexa --noclipping
COMMON_SETTINGS -GE:number_of_threads=8 -MI:stop_on_nfs=no:somrnl=0
SOLEXA_SETTINGS -LR:file_type=fastq
I am having to run it on a NFS but that cannot be the problem. MIRA stops
due to an internal error ("Error while loading adsfacts, less facts in file
than calculated earlier!"). It was using <30 GB or RAM at that point so
memory is not an issue. Any ideas about what could be going on? The STDOUT
is pasted below. Thanks!
-Surya
This is MIRA V3.4.0 (production version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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Compiled by: bach
Sun Aug 21 17:50:30 CEST 2011
On: Linux arcadia 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC
2011 x86_64 x86_64 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux lmcompute-4-4.v4linux 2.6.18-238.19.1.el5 #1 SMP Fri
Jul 15 07:31:24 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=9gb_28e6_def
--job=denovo,genome,accurate,solexa --noclipping COMMON_SETTINGS
-GE:number_of_threads=8 -MI:stop_on_nfs=no:somrnl=0 SOLEXA_SETTINGS
-LR:file_type=fastq
Using quickmode switch -noclipping :
SANGER_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:c3pp=no:cpat=no:mqtfer=0:ckar=no
454_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:c3pp=no:cpat=no:mqtfer=0:ckar=no
IONTOR_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:c3pp=no:cpat=no:mqtfer=0:ckar=no
PACBIO_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:c3pp=no:cpat=no:mqtfer=0:ckar=no
SOLEXA_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:c3pp=no:cpat=no:mqtfer=0:ckar=no
SOLID_SETTINGS
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:lcc=no:emlc=no:emrc=no:c3pp=no:cpat=no:mqtfer=0:ckar=no
COMMON_SETTINGS -CL:ascdc=no:asjdc=no:cbse=no
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), Solexa data
Used parameter settings:
General (-GE):
Project name in (proin) : 9gb_28e6_def
Project name out (proout) : 9gb_28e6_def
Number of threads (not) : 8
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[sxa] yes
Template insert size minimum (tismin) : [san] -1
[sxa] -1
Template insert size maximum (tismax) : [san] -1
[sxa] -1
Template partner build direction (tpbd) : [san] -1
[sxa] -1
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] no
[sxa] yes
File type (ft) : [san] fasta
[sxa] fastq
External quality (eq) : from SCF (scf)
Ext. qual. override (eqo) : no
Discard reads on e.q. error (droeqe): no
Solexa scores in qual file (ssiqf) : no
FASTQ qual offset (fqqo) : [san] 0
[sxa] 0
Wants quality file (wqf) : [san] yes
[sxa] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[sxa] Solexa (solexa)
Merge with XML trace info (mxti) : [san] no
[sxa] no
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 3
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 1
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [san] 80
[sxa] 20
Minimum reads per contig (mrpc) : [san] 2
[sxa] 10
Base default quality (bdq) : [san] 10
[sxa] 10
Enforce presence of qualities (epoq) : [san] yes
[sxa] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[sxa] 2.5
Minimum length (ardml) : [san] 400
[sxa] 300
Grace length (ardgl) : [san] 40
[sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [san] 1.5
[sxa] 1.5
Keep long repeats separated (klrs) : no
Spoiler detection (sd) : 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
[sxa] no
Default strain name (dsn) : [san] 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
[sxa] no
Read extension window length (rewl) : [san] 30
[sxa] 30
Read extension w. maxerrors (rewme) : [san] 2
[sxa] 2
First extension in pass (feip) : [san] 0
[sxa] 0
Last extension in pass (leip) : [san] 0
[sxa] 0
Clipping options (-CL):
Merge with SSAHA2/SMALT vector screen (msvs): [san] no
[sxa] no
Gap size (msvsgs) : [san] 10
[sxa] 1
Max front gap (msvsmfg) : [san] 60
[sxa] 2
Max end gap (msvsmeg) : [san] 120
[sxa] 2
Strict front clip (msvssfc) : [san] 0
[sxa] 0
Strict end clip (msvssec) : [san] 0
[sxa] 0
Possible vector leftover clip (pvlc) : [san] no
[sxa] no
maximum len allowed (pvcmla) : [san] 18
[sxa] 18
Min qual. threshold for entire read (mqtfer): [san] 0
[sxa] 0
Number of bases (mqtfernob) : [san] 0
[sxa] 15
Quality clip (qc) : [san] no
[sxa] no
Minimum quality (qcmq) : [san] 20
[sxa] 20
Window length (qcwl) : [san] 30
[sxa] 30
Bad stretch quality clip (bsqc) : [san] no
[sxa] no
Minimum quality (bsqcmq) : [san] 20
[sxa] 5
Window length (bsqcwl) : [san] 30
[sxa] 20
Masked bases clip (mbc) : [san] no
[sxa] no
Gap size (mbcgs) : [san] 20
[sxa] 5
Max front gap (mbcmfg) : [san] 40
[sxa] 12
Max end gap (mbcmeg) : [san] 60
[sxa] 12
Lower case clip (lcc) : [san] no
[sxa] no
Clip poly A/T at ends (cpat) : [san] no
[sxa] no
Keep poly-a signal (cpkps) : [san] no
[sxa] no
Minimum signal length (cpmsl) : [san] 12
[sxa] 12
Max errors allowed (cpmea) : [san] 1
[sxa] 1
Max gap from ends (cpmgfe) : [san] 9
[sxa] 9
Clip 3 prime polybase (c3pp) : [san] no
[sxa] no
Minimum signal length (c3ppmsl) : [san] 12
[sxa] 12
Max errors allowed (c3ppmea) : [san] 2
[sxa] 2
Max gap from ends (c3ppmgfe) : [san] 9
[sxa] 9
Clip known adaptors right (ckar) : [san] no
[sxa] no
Ensure minimum left clip (emlc) : [san] no
[sxa] no
Minimum left clip req. (mlcr) : [san] 25
[sxa] 0
Set minimum left clip to (smlc) : [san] 30
[sxa] 0
Ensure minimum right clip (emrc) : [san] no
[sxa] no
Minimum right clip req. (mrcr) : [san] 10
[sxa] 10
Set minimum right clip to (smrc) : [san] 20
[sxa] 20
Apply SKIM chimera detection clip (ascdc) : no
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : yes
Bases per hash (pecbph) : 31
Handle Solexa GGCxG problem (pechsgp) : yes
Clip bad solexa ends (cbse) : no
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 8
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 17
Hash save stepping (hss) : 1
Percent required (pr) : [san] 65
[sxa] 95
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : no
Freq. est. min normal (fenn) : 0.4
Freq. est. max normal (fexn) : 1.6
Freq. est. repeat (fer) : 1.9
Freq. est. heavy repeat (fehr) : 8
Freq. est. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 100
Repeat level in info file (rliif) : 6
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 4096
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[sxa] yes
Quick rule min len 1 (qrml1) : [san] 200
[sxa] -95
Quick rule min sim 1 (qrms1) : [san] 90
[sxa] 100
Quick rule min len 2 (qrml2) : [san] 100
[sxa] -85
Quick rule min sim 2 (qrms2) : [san] 95
[sxa] 100
Backbone quick overlap min len (bqoml) : [san] 150
[sxa] 20
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[sxa] 20
Bandwidth max (bmax) : [san] 130
[sxa] 80
Bandwidth min (bmin) : [san] 25
[sxa] 20
Minimum score (ms) : [san] 30
[sxa] 15
Minimum overlap (mo) : [san] 17
[sxa] 25
Minimum relative score in % (mrs) : [san] 65
[sxa] 90
Solexa_hack_max_errors (shme) : [san] 0
[sxa] 0
Extra gap penalty (egp) : [san] no
[sxa] no
extra gap penalty level (egpl) : [san] low
[sxa] low
Max. egp in percent (megpp) : [san] 100
[sxa] 100
Contig parameters (-CO):
Name prefix (np) : 9gb_28e6_def
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[sxa] 30
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[sxa] 4
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[sxa] 30
End-read Marking Exclusion Area in bases (emea) : [san] 1
[sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[sxa] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[sxa] no
Merge short reads (msr) : [san] no
[sxa] yes
Keep ends unmerged (msrkeu) : [san] -1
[sxa] -1
Gap override ratio (gor) : [san] 66
[sxa] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[sxa] no
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Misc (-MI):
Stop on NFS (sonfs) : no
Extended log (el) : no
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 5000
Stop on max read name length (somrnl) : 0
Directories (-DI):
Working directory :
When loading EXP files :
When loading SCF files :
Top directory for writing files : 9gb_28e6_def_assembly
For writing result files :
9gb_28e6_def_assembly/9gb_28e6_def_d_results
For writing result info files :
9gb_28e6_def_assembly/9gb_28e6_def_d_info
For writing tmp files :
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files :
9gb_28e6_def_assembly/9gb_28e6_def_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
9gb_28e6_def_in.sanger.fasta
[sxa]
9gb_28e6_def_in.solexa.fasta
When loading qualities from FASTA quality : [san]
9gb_28e6_def_in.sanger.fasta.qual
[sxa]
9gb_28e6_def_in.solexa.fasta.qual
When loading sequences from FASTQ : [san]
9gb_28e6_def_in.sanger.fastq
[sxa]
9gb_28e6_def_in.solexa.fastq
When loading project from CAF :
9gb_28e6_def_in.sanger.caf
When loading project from MAF (disabled) :
9gb_28e6_def_in.sanger.maf
When loading EXP fofn :
9gb_28e6_def_in.sanger.fofn
When loading project from PHD : 9gb_28e6_def_in.phd.1
When loading strain data :
9gb_28e6_def_straindata_in.txt
When loading XML trace info files : [san]
9gb_28e6_def_traceinfo_in.sanger.xml
[sxa]
9gb_28e6_def_traceinfo_in.solexa.xml
When loading SSAHA2 vector screen results :
9gb_28e6_def_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
9gb_28e6_def_smaltvectorscreen_in.txt
When loading backbone from MAF :
9gb_28e6_def_backbone_in.maf
When loading backbone from CAF :
9gb_28e6_def_backbone_in.caf
When loading backbone from GenBank :
9gb_28e6_def_backbone_in.gbf
When loading backbone from GFF3 :
9gb_28e6_def_backbone_in.gff3
When loading backbone from FASTA :
9gb_28e6_def_backbone_in.fasta
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[sxa] no
Save tagged singlets in project (stsip) : [san] yes
[sxa] yes
Remove rollover tmps (rrot) : yes
Remove tmp directory (rtd) : 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 : 9gb_28e6_def_out.caf
MAF : 9gb_28e6_def_out.maf
FASTA : 9gb_28e6_def_out.unpadded.fasta
FASTA quality : 9gb_28e6_def_out.unpadded.fasta.qual
FASTA (padded) : 9gb_28e6_def_out.padded.fasta
FASTA qual.(pad): 9gb_28e6_def_out.padded.fasta.qual
GAP4 (directory): 9gb_28e6_def_out.gap4da
ACE : 9gb_28e6_def_out.ace
HTML : 9gb_28e6_def_out.html
Simple text : 9gb_28e6_def_out.txt
TCS overview : 9gb_28e6_def_out.tcs
Wiggle : 9gb_28e6_def_out.wig
------------------------------------------------------------------------------
Creating directory 9gb_28e6_def_assembly ... done.
Creating directory 9gb_28e6_def_assembly/9gb_28e6_def_d_tmp ... done.
Creating directory 9gb_28e6_def_assembly/9gb_28e6_def_d_results ... done.
Creating directory 9gb_28e6_def_assembly/9gb_28e6_def_d_info ... done.
Creating directory 9gb_28e6_def_assembly/9gb_28e6_def_d_chkpt ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Thu Aug 25 10:19:49 2011
Loading data (Solexa) from FASTQ files,
Localtime: Thu Aug 25 10:19:49 2011
Counting sequences in FASTQ file: found 14000000 sequences.
Localtime: Thu Aug 25 10:20:05 2011
Solexa will load 14000000 reads.
Longest Sanger: 0
Longest 454: 0
Longest IonTor: 0
Longest PacBio: 0
Longest Solexa: 100
Longest Solid: 0
Longest overall: 100
Total reads to load: 14000000
Reserving space for reads (this may take a while)
Reserved space for 14000010 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Thu Aug 25 10:20:05 2011
Counting sequences in FASTQ file: found 14000000 sequences.
Localtime: Thu Aug 25 10:20:21 2011
Using calculated FASTQ quality offset: 66
Localtime: Thu Aug 25 10:20:21 2011
Loading data from FASTQ file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Done.
Loaded 14000000 reads, Localtime: Thu Aug 25 10:21:20 2011
Loaded 14000000 Solexa reads.
Total reads loaded: 14000000
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.
14000000 reads with valid data for assembly.
Localtime: Thu Aug 25 10:21:35 2011
Generated 7000000 unique template ids for 14000000 valid reads.
Localtime: Thu Aug 25 10:22:07 2011
Generated 0 unique strain ids for 14000000 reads.
Strain "default" has 14000000 reads.
Have read pool with 14000000 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 14000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 14000000 0
Avg tot rlen 0 0 0 0 88 0
Avg rlen used 0 0 0 0 87 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 14000000 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:1238800892 used bases in used reads: 1224800892
Solid total bases:0 used bases in used reads: 0
===========================================================================
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 14000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 14000000 0
Avg tot rlen 0 0 0 0 88 0
Avg rlen used 0 0 0 0 87 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 14000000 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:1238800892 used bases in used reads: 1224800892
Solid total bases:0 used bases in used reads: 0
===========================================================================
Tmp directory is not on a NFS mount, good.
Hash analysis for proposed cutbacks:Localtime: Thu Aug 25 10:22:25 2011
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Localtime: Thu Aug 25 10:26:53 2011
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Thu Aug 25 10:34:13 2011
clean up temporary stat files...Localtime: Thu Aug 25 10:34:34 2011
Localtime: Thu Aug 25 10:34:41 2011
Hash statistics:
=========================================================
Measured avg. frequency coverage: 131
Deduced thresholds:
-------------------
Min normal cov: 52.4
Max normal cov: 209.6
Repeat cov: 248.9
Heavy cov: 1048
Crazy cov: 2620
Mask cov: 13100
Repeat ratio histogram:
-----------------------
0 4687450
1 8913532
2 1264412
3 148666
4 46536
5 23400
6 13612
7 8478
8 5394
9 4072
10 1456
11 628
12 256
13 274
14 360
15 232
16 200
17 276
18 166
19 150
20 260
21 228
22 146
23 178
24 246
25 140
26 178
27 214
28 136
29 82
30 40
31 50
32 104
33 64
34 14
35 26
36 28
37 72
38 64
39 50
40 38
41 40
42 16
43 34
44 14
60 2
61 10
62 4
=========================================================
Assigning statistics values:
Localtime: Thu Aug 25 10:34:41 2011
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Thu Aug 25 10:41:36 2011
Localtime: Thu Aug 25 10:41:36 2011
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 19717
Num reads cliped right: 253190
Num reads completely killed: 3410
Total bases clipped : 2929488
Clipping dubious poly-base stretches at end of reads ... done.
Hash analysis for proposed cutbacks:Localtime: Thu Aug 25 10:41:51 2011
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Localtime: Thu Aug 25 10:44:06 2011
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Thu Aug 25 10:51:34 2011
clean up temporary stat files...Localtime: Thu Aug 25 10:51:55 2011
Localtime: Thu Aug 25 10:52:02 2011
Hash statistics:
=========================================================
Measured avg. frequency coverage: 132
Deduced thresholds:
-------------------
Min normal cov: 52.8
Max normal cov: 211.2
Repeat cov: 250.8
Heavy cov: 1056
Crazy cov: 2640
Mask cov: 13200
Repeat ratio histogram:
-----------------------
0 3563778
1 8937479
2 1241779
3 145600
4 45534
5 23238
6 13478
7 8282
8 5330
9 3870
10 1392
11 532
12 264
13 270
14 374
15 212
16 216
17 262
18 162
19 170
20 264
21 210
22 152
23 190
24 242
25 140
26 172
27 214
28 118
29 76
30 44
31 68
32 102
33 36
34 22
35 22
36 48
37 66
38 62
39 36
40 54
41 26
42 22
43 30
44 8
60 8
61 8
=========================================================
Assigning statistics values:
Localtime: Thu Aug 25 10:52:02 2011
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Thu Aug 25 10:58:51 2011
Localtime: Thu Aug 25 10:58:51 2011
Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 747
Num reads cliped right: 3948
Num reads completely killed: 111
Total bases clipped : 38308
Clipping dubious poly-base stretches at end of reads ... done.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 14000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 13996386 0
Avg tot rlen 0 0 0 0 88 0
Avg rlen used 0 0 0 0 87 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 13726232 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:1238800892 used bases in used reads: 1221772035
Solid total bases:0 used bases in used reads: 0
===========================================================================
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 0%
Tgid: 28680
Pid: 28680
PPid: 28674
TracerPid: 0
Uid: 16777813 16777813 16777813 16777813
Gid: 10000 10000 10000 10000
FDSize: 256
Groups: 10000 10157 10321
VmPeak: 15787988 kB
VmSize: 15787924 kB
VmLck: 0 kB
VmHWM: 15587236 kB
VmRSS: 15587068 kB
VmData: 15782564 kB
VmStk: 88 kB
VmExe: 5236 kB
VmLib: 0 kB
VmPTE: 30488 kB
StaBrk: 036cb000 kB
Brk: 3c6b0c000 kB
StaStk: 7ffff20e63e0 kB
Threads: 1
SigQ: 0/530432
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000001000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,ffffffff
Mems_allowed: 00000000,00000001
--------------------------------------------------------------------------------
Pass: 1 / 3
Performing snapshot 1
Localtime: Thu Aug 25 10:59:09 2011
Localtime: Thu Aug 25 11:00:45 2011
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PacBio Solexa SOLiD
----------------------------------------
Total reads 0 0 0 0 14000000 0
Reads wo qual 0 0 0 0 0 0
Used reads 0 0 0 0 13996386 0
Avg tot rlen 0 0 0 0 88 0
Avg rlen used 0 0 0 0 87 0
With strain 0 0 0 0 0 0
W/o clips 0 0 0 0 13726232 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PacBio total bases:0 used bases in used reads: 0
Solexa total bases:1238800892 used bases in used reads: 1221772035
Solid total bases:0 used bases in used reads: 0
===========================================================================
Localtime: Thu Aug 25 11:00:48 2011
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done
Localtime: Thu Aug 25 11:03:49 2011
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Thu Aug 25 11:13:08 2011
clean up temporary stat files...Localtime: Thu Aug 25 11:13:34 2011
Localtime: Thu Aug 25 11:13:40 2011
Hash statistics:
=========================================================
Measured avg. frequency coverage: 162
Deduced thresholds:
-------------------
Min normal cov: 64.8
Max normal cov: 259.2
Repeat cov: 307.8
Heavy cov: 1296
Crazy cov: 3240
Mask cov: 16200
Repeat ratio histogram:
-----------------------
0 2761088
1 9185807
2 1214837
3 148260
4 50870
5 27552
6 15636
7 9168
8 6502
9 4004
10 1520
11 868
12 352
13 330
14 400
15 226
16 300
17 304
18 328
19 194
20 268
21 218
22 214
23 278
24 246
25 168
26 216
27 210
28 122
29 84
30 46
31 96
32 100
33 74
34 16
35 40
36 86
37 80
38 52
39 20
40 104
41 14
42 32
43 42
46 2
48 2
49 4
50 2
52 2
53 2
55 2
60 2
61 2
66 4
69 8
70 4
72 2
81 2
85 2
88 2
=========================================================
Assigning statistics values:
Localtime: Thu Aug 25 11:13:40 2011
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Localtime: Thu Aug 25 11:21:56 2011
Buntifying reads (this may take a while) ... done.
Writing read repeat info to:
9gb_28e6_def_assembly/9gb_28e6_def_d_info/9gb_28e6_def_info_readrepeats.lst
... 156402 sequences with 187550 masked stretches.
Localtime: Thu Aug 25 11:22:28 2011
Searching for possible overlaps:
Localtime: Thu Aug 25 11:22:28 2011
Now running threaded and partitioned skimmer with 82 partitions in 8
threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ..truncating
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp/9gb_28e6_def_int_posmatchf_pass.1.bin
from 11138087184 to 8823555000
.truncating
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp/9gb_28e6_def_int_posmatchc_pass.1.bin
from 10756888968 to 8690135736
.|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] .truncating
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp/9gb_28e6_def_int_posmatchf_pass.1.bin
from 21705369888 to 18382481664
..truncating
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp/9gb_28e6_def_int_posmatchc_pass.1.bin
from 21559777416 to 18455396856
.|.... [80%] ....|.... [90%] ....|.... [100%] done.
truncating
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp/9gb_28e6_def_int_posmatchf_pass.1.bin
from 27265753872 to 24855669672
truncating
9gb_28e6_def_assembly/9gb_28e6_def_d_tmp/9gb_28e6_def_int_posmatchc_pass.1.bin
from 26681440536 to 24590752800
Skim summary:
accepted: 2954471258
possible: 201784884
permbans: 0
Hits chosen: 2698156192
Localtime: Thu Aug 25 15:19:23 2011
Total megahubs: 0
System memory: 67587063808
Mem2keepfree: 10138059571
Used by MIRA: 19259060224
Mem avail: 38189944013
rsh increased memtouse to: 38189944013
Can load up to 563714375 skim edges at once.
Partitioning into 8 blocks.
We have 4120535206 skims in file.
Localtime: Thu Aug 25 15:19:26 2011
De-normalising SKIM hits ... (this will take a while)
Loading skims in id range 0 to 943933
Localtime: Thu Aug 25 15:24:55 2011
Loaded 536870834 elements.
Sorting ... done.
Localtime: Thu Aug 25 15:29:14 2011
Writing normalised skimblock 0 ( 16.0 GiB) ... done.
Loading skims in id range 943934 to 1966089
Localtime: Thu Aug 25 15:38:35 2011
Loaded 536870748 elements.
Sorting ... done.
Localtime: Thu Aug 25 15:42:54 2011
Writing normalised skimblock 943934 ( 16.0 GiB) ... done.
Loading skims in id range 1966090 to 3068540
Localtime: Thu Aug 25 15:52:21 2011
Loaded 536870088 elements.
Sorting ... done.
Localtime: Thu Aug 25 15:56:39 2011
Writing normalised skimblock 1966090 ( 16.0 GiB) ... done.
Loading skims in id range 3068541 to 4304483
Localtime: Thu Aug 25 16:06:07 2011
Loaded 536870724 elements.
Sorting ... done.
Localtime: Thu Aug 25 16:10:22 2011
Writing normalised skimblock 3068541 ( 16.0 GiB) ... done.
Loading skims in id range 4304484 to 5725668
Localtime: Thu Aug 25 16:19:37 2011
Loaded 536870440 elements.
Sorting ... done.
Localtime: Thu Aug 25 16:23:56 2011
Writing normalised skimblock 4304484 ( 16.0 GiB) ... done.
Loading skims in id range 5725669 to 7463490
Localtime: Thu Aug 25 16:33:12 2011
Loaded 536870762 elements.
Sorting ... done.
Localtime: Thu Aug 25 16:37:37 2011
Writing normalised skimblock 5725669 ( 16.0 GiB) ... done.
Loading skims in id range 7463491 to 9849829
Localtime: Thu Aug 25 16:47:12 2011
Loaded 536870762 elements.
Sorting ... done.
Localtime: Thu Aug 25 16:51:35 2011
Writing normalised skimblock 7463491 ( 16.0 GiB) ... done.
Loading skims in id range 9849830 to 13999999
Localtime: Thu Aug 25 17:01:44 2011
Loaded 362440848 elements.
Sorting ... done.
Localtime: Thu Aug 25 17:04:33 2011
Writing normalised skimblock 9849830 ( 10.8 GiB) ... done.
Localtime: Thu Aug 25 17:07:01 2011
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
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Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
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Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Localtime: Thu Aug 25 17:25:37 2011
Step 0
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
Loading 536870088 elements at offset 34359730624
Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
Loading 536870440 elements at offset 68719436608
Loaded 536870440 elements
Loading block 5
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Loaded 536870762 elements
Loading block 6
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Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Localtime: Thu Aug 25 17:58:10 2011
Only short reads
Step 10
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
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Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
Loading 536870440 elements at offset 68719436608
Loaded 536870440 elements
Loading block 5
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Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 43278705
Step 20
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
Loading 536870088 elements at offset 34359730624
Loaded 536870088 elements
Loading block 3
Loading 536870724 elements at offset 51539573440
Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 94355820
Step 30
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
Loading 536870088 elements at offset 34359730624
Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
Loading 536870440 elements at offset 68719436608
Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 94355820
Step 40
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
Loading 536870088 elements at offset 34359730624
Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
Loading 536870440 elements at offset 68719436608
Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 94355820
Step 50
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
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Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 604663052
Step 55
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
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Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 613899161
Step 56
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
Loading 536870088 elements at offset 34359730624
Loaded 536870088 elements
Loading block 3
Loading 536870724 elements at offset 51539573440
Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 613926272
Step 60
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
Loading 536870748 elements at offset 17179866688
Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Total skims taken: 613936555
Step solexa by critlevel
rsh4_takeSolexaByCritLevel.
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
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Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
Loading 536870440 elements at offset 68719436608
Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Taken 26995105 hits.
Step template overlaps
Loading block 0
Loading 536870834 elements at offset 0
Loaded 536870834 elements
Loading block 1
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Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
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Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
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Loaded 362440848 elements
Step NAO
rsh4_takeNeedAllOverlaps.
Loading block 0
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Loaded 536870834 elements
Loading block 1
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Loaded 536870748 elements
Loading block 2
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Loaded 536870088 elements
Loading block 3
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Loaded 536870724 elements
Loading block 4
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Loaded 536870440 elements
Loading block 5
Loading 536870762 elements at offset 85899290688
Loaded 536870762 elements
Loading block 6
Loading 536870762 elements at offset 103079155072
Loaded 536870762 elements
Loading block 7
Loading 362440848 elements at offset 120259019456
Loaded 362440848 elements
Taken 0 hits.
Total skims taken: 642968188
Filtering forward skims.
Localtime: Thu Aug 25 22:03:31 2011
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Done.
Done.
Filtering complement skims.
Localtime: Thu Aug 25 22:17:47 2011
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Done.
Done all filtering.
Localtime: Thu Aug 25 22:31:41 2011
Making alignments.
Localtime: Thu Aug 25 22:31:47 2011
Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Alignment stats:
Potential: 338871153
Calculated: 9468
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 338861684
Banned overlap pairs: 349 in 127 sets.
Localtime: Thu Aug 25 22:49:50 2011
Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Alignment stats:
Potential: 304097035
Calculated: 37183
Evaded (PB): 54
Rejected (checkfun): 0
Trans 100 saved: 304059796
Banned overlap pairs: 931 in 508 sets.
Localtime: Thu Aug 25 23:01:19 2011
Localtime: Thu Aug 25 23:01:19 2011
Counting number of alignments in file ... done.
Expecting 512423414 alignments.
Localtime: Thu Aug 25 23:03:51 2011
Loading confirmed overlaps from disk (will need approximately 28.6 GiB RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"Error while loading adsfacts, less facts in file than calculated earlier!"
->Thrown: void Assembly::loadAlignmentsFromFile(int32 version, const string
prefix, const string postfix, const string tmpfname)
->Caught: void Assembly::loadAlignmentsFromFile(int32 version, const string
prefix, const string postfix, const string tmpfname)
Aborting process, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/apps/trac/mira-assembler/
and also give a short notice on the mira talk mailing list.
If reporting, please do not delete the log and checkpoint directories, there
may
be files in them which could be needed to find the problem.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /tmp/1106239.scheduler.v4linux
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Other related posts:
