[mira_talk] Re: Out of memory detected, exception message is: std::bad_alloc
- From: joel klein <joel.klein@xxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Mar 2013 16:33:52 +0800
Dear Mira users,
I want to use Mira assembler to assembly a whole potato genome based
on 454 and Solexa data. To test the assembler I first tried to map the
Solexa reads against a reference genome in Genbank format. However
when I run the Mira program after a few hours it terminates with an
out of memory error. I tried to avoid the problem by switching off the
Automatic memory management (amm) or increase the Keep percent memory
free (kpmf). Unfortunatly this does not solve the problem and Im
afraid if I will use Mira as an denovo assembler I will run into the
same problem.
Thank you in advance,
Joel Klein
Chinese academy of Sciences, Beijing China
Ps these are the files in the directory I'm running the program in:
drwxrwxr-x. 6 joel joel 4096 Mar 14 15:48 Potatomap_assembly
-rw-rw-r--. 1 joel joel 819755346 Mar 2 16:24 Potatomap_backbone_in.gbf
This is MIRA V3.4.1.1 (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: root
Fri Mar 1 21:57:31 CST 2013
On: Linux localhost 2.6.32-279.22.1.el6.centos.plus.x86_64 #1 SMP Wed
Feb 6 05:16:56 UTC 2013 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 localhost 2.6.32-279.22.1.el6.centos.plus.x86_64
#1 SMP Wed Feb 6 05:16:56 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=Potatomap
--job=mapping,genome,accurate,solexa -GE:not=20 -AS:nop=1
-SB:lsd=yes:bsn=Potatomap_wt:bft=gbf:bbq=30 SOLEXA_SETTINGS -CO:msr=no
-GE:uti=no:tismin=250:tismax=750 -SB:ads=yes:dsn=Potatomap
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) : Potatomap
Project name out (proout) : Potatomap
Number of threads (not) : 20
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[sxa] no
Template insert size minimum (tismin) : [san] -1
[sxa] 250
Template insert size maximum (tismax) : [san] -1
[sxa] 750
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) : 1
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
Minimum length (ardml) : [san] 400
[sxa] 200
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) : yes
Assign default strain (ads) : [san] no
[sxa] yes
Default strain name (dsn) : [san] StrainX
[sxa] Potatomap
Load backbone (lb) : yes
Start backbone usage in pass (sbuip) : 0
Backbone file type (bft) : gbf
Backbone base quality (bbq) : 30
Backbone strain name (bsn) : Potatomap_wt
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) : no
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] yes
[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] yes
[sxa] no
Minimum quality (bsqcmq) : [san] 20
[sxa] 5
Window length (bsqcwl) : [san] 30
[sxa] 20
Masked bases clip (mbc) : [san] yes
[sxa] no
Gap size (mbcgs) : [san] 20
[sxa] 5
Max front gap (mbcmfg) : [san] 40
[sxa] 12
Max end gap (mbcmeg) : [san] 60
[sxa] 12
Lower case clip (lcc) : [san] no
[sxa] no
Clip poly A/T at ends (cpat) : [san] no
[sxa] no
Keep poly-a signal (cpkps) : [san] no
[sxa] no
Minimum signal length (cpmsl) : [san] 12
[sxa] 12
Max errors allowed (cpmea) : [san] 1
[sxa] 1
Max gap from ends (cpmgfe) : [san] 9
[sxa] 9
Clip 3 prime polybase (c3pp) : [san] no
[sxa] yes
Minimum signal length (c3ppmsl) : [san] 12
[sxa] 12
Max errors allowed (c3ppmea) : [san] 2
[sxa] 2
Max gap from ends (c3ppmgfe) : [san] 9
[sxa] 9
Clip known adaptors right (ckar) : [san] no
[sxa] yes
Ensure minimum left clip (emlc) : [san] yes
[sxa] no
Minimum left clip req. (mlcr) : [san] 25
[sxa] 0
Set minimum left clip to (smlc) : [san] 30
[sxa] 0
Ensure minimum right clip (emrc) : [san] no
[sxa] no
Minimum right clip req. (mrcr) : [san] 10
[sxa] 10
Set minimum right clip to (smrc) : [san] 20
[sxa] 20
Apply SKIM chimera detection clip (ascdc) : 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) : yes
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 20
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 10
Hash save stepping (hss) : 1
Percent required (pr) : [san] 60
[sxa] 60
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : yes
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) : no
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] -90
Quick rule min sim 1 (qrms1) : [san] 90
[sxa] 100
Quick rule min len 2 (qrml2) : [san] 100
[sxa] -80
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] 20
Minimum relative score in % (mrs) : [san] 65
[sxa] 60
Solexa_hack_max_errors (shme) : [san] -1
[sxa] -1
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) : Potatomap
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[sxa] 30
Mark repeats (mr) : yes
Only in result (mroir) : yes
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[sxa] 3
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[sxa] 30
End-read Marking Exclusion Area in bases (emea) : [san] 1
[sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[sxa] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[sxa] no
Merge short reads (msr) : [san] no
[sxa] no
Keep ends unmerged (msrkeu) : [san] -1
[sxa] -1
Gap override ratio (gor) : [san] 66
[sxa] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[sxa] no
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Misc (-MI):
Stop on NFS (sonfs) : yes
Extended log (el) : no
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 5000
Stop on max read name length (somrnl) : 40
Directories (-DI):
Working directory :
When loading EXP files :
When loading SCF files :
Top directory for writing files : Potatomap_assembly
For writing result files :
Potatomap_assembly/Potatomap_d_results
For writing result info files : Potatomap_assembly/Potatomap_d_info
For writing tmp files : Potatomap_assembly/Potatomap_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : Potatomap_assembly/Potatomap_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
Potatomap_in.sanger.fasta
[sxa]
Potatomap_in.solexa.fasta
When loading qualities from FASTA quality : [san]
Potatomap_in.sanger.fasta.qual
[sxa]
Potatomap_in.solexa.fasta.qual
When loading sequences from FASTQ : [san]
Potatomap_in.sanger.fastq
[sxa]
Potatomap_in.solexa.fastq
When loading project from CAF : Potatomap_in.sanger.caf
When loading project from MAF (disabled) : Potatomap_in.sanger.maf
When loading EXP fofn : Potatomap_in.sanger.fofn
When loading project from PHD : Potatomap_in.phd.1
When loading strain data :
Potatomap_straindata_in.txt
When loading XML trace info files : [san]
Potatomap_traceinfo_in.sanger.xml
[sxa]
Potatomap_traceinfo_in.solexa.xml
When loading SSAHA2 vector screen results :
Potatomap_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
Potatomap_smaltvectorscreen_in.txt
When loading backbone from MAF : Potatomap_backbone_in.maf
When loading backbone from CAF : Potatomap_backbone_in.caf
When loading backbone from GenBank : Potatomap_backbone_in.gbf
When loading backbone from GFF3 :
Potatomap_backbone_in.gff3
When loading backbone from FASTA :
Potatomap_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 : Potatomap_out.caf
MAF : Potatomap_out.maf
FASTA : Potatomap_out.unpadded.fasta
FASTA quality : Potatomap_out.unpadded.fasta.qual
FASTA (padded) : Potatomap_out.padded.fasta
FASTA qual.(pad): Potatomap_out.padded.fasta.qual
GAP4 (directory): Potatomap_out.gap4da
ACE : Potatomap_out.ace
HTML : Potatomap_out.html
Simple text : Potatomap_out.txt
TCS overview : Potatomap_out.tcs
Wiggle : Potatomap_out.wig
------------------------------------------------------------------------------
Deleting old directory Potatomap_assembly ... done.
Creating directory Potatomap_assembly ... done.
Creating directory Potatomap_assembly/Potatomap_d_tmp ... done.
Creating directory Potatomap_assembly/Potatomap_d_results ... done.
Creating directory Potatomap_assembly/Potatomap_d_info ... done.
Creating directory Potatomap_assembly/Potatomap_d_chkpt ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Wed Mar 6 21:50:53 2013
Loading backbone from GBF file: Potatomap_backbone_in.gbf
Localtime: Wed Mar 6 21:53:15 2013
Generated 0 unique strain ids for 12 reads.
Done.
Adding sequences as backbones ... done.
Postprocessing backbone(s) ... this may take a while.
12 to process
chr01_bb 81482218
chr02_bb 47066339
chr03_bb 47880312
chr04_bb 64339883
chr05_bb 47045015
chr06_bb 54975350
chr07_bb 53427889
chr08_bb 43648432
chr09_bb 53640104
chr10_bb 52313507
chr11_bb 42253929
chr12_bb 59100875
Strain "default" has 12 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Wed Mar 6 21:58:48 2013
Counting sequences in FASTQ file: found 1583666226 sequences.
Localtime: Wed Mar 6 22:49:06 2013
Solexa will load 1583666226 reads.
Longest Sanger: 0
Longest 454: 0
Longest IonTor: 0
Longest PacBio: 0
Longest Solexa: 75
Longest Solid: 0
Longest overall: 75
Total reads to load: 1583666226
-AL:shme is <0, automatically determining optimal value.
set -AL:shme 11
-SB:brl is 0, automatically determining optimal value.
brl: 172
-SB:bro is 0, automatically determining optimal value.
bro: 86
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
makeIntelligentConsensus() complete calc
Reserving space for reads (this may take a while)
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 140433584 kB
MemFree: 2339944 kB
Buffers: 642316 kB
Cached: 58669384 kB
SwapCached: 56964 kB
Active: 78543716 kB
Inactive: 55517588 kB
Active(anon): 71423140 kB
Inactive(anon): 3327200 kB
Active(file): 7120576 kB
Inactive(file): 52190388 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 150994936 kB
SwapFree: 150729380 kB
Dirty: 94140 kB
Writeback: 0 kB
AnonPages: 74893612 kB
Mapped: 20292 kB
Shmem: 12 kB
Slab: 2186144 kB
SReclaimable: 2096852 kB
SUnreclaim: 89292 kB
KernelStack: 6648 kB
PageTables: 167500 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 221211728 kB
Committed_AS: 75697544 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 714952 kB
VmallocChunk: 34290457780 kB
HardwareCorrupted: 276 kB
AnonHugePages: 20023296 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
DirectMap4k: 5504 kB
DirectMap2M: 2082816 kB
DirectMap1G: 140509184 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 22263
Pid: 22263
PPid: 22239
TracerPid: 0
Uid: 512 512 512 512
Gid: 514 514 514 514
Utrace: 0
FDSize: 256
Groups: 514
VmPeak: 68781076 kB
VmSize: 68384884 kB
VmLck: 0 kB
VmHWM: 68662152 kB
VmRSS: 68200576 kB
VmData: 68323136 kB
VmStk: 88 kB
VmExe: 3252 kB
VmLib: 23308 kB
VmPTE: 133512 kB
VmSwap: 59984 kB
Threads: 1
SigQ: 0/1096978
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ffffff
Cpus_allowed_list: 0-23
Mems_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
Mems_allowed_list: 0-1
voluntary_ctxt_switches: 170260
nonvoluntary_ctxt_switches: 742347
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 12 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 12 contigs.
Mem used for reads: 5824570920 (5.4 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_usedtmpfiles: 1 48 B 0 B 0 B
Total: 5824571728 (5.4 GiB)
================================================================================
Dynamic allocs: 0
Align allocs: 0
Out of memory detected, exception message is: std::bad_alloc
If you have questions on why this happened, please send the last 1000
lines of the output log (or better: the complete file) to the author
together with a short summary of your assembly project.
For general help, you will probably get a quicker response on the
MIRA talk mailing list
than if you mailed the author directly.
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.
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