[mira_talk] Out of memory when lots of memory available...
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 01 Jul 2010 09:17:01 +0200
Hi!
I'm using mira 3.1.15 to assemble de novo a small (1.6 Mb) bacterial
genome, with an acceptable level of repeats (had 1-2 megahubs). I'm
using paired-end and non-paired-end 454 reads (300 kreads) and some long
Sanger reads (separate fosmid assemblies, 5-20kb long).
I've already been running a very similar assembly (but with less Sanger
reads) earlier with a previous version of mira (3.0.4, if I remember
correctly), and had no particular problems.
Now I'm running it again and got three times out of memory troubles, at
different points of the assembly, and running it on different machines
(twice on a local machine with 8Gb, and once on a cluster node with 24
Gb).
I got this on the standard error:
tcmalloc: large alloc 2176647168 bytes == 0x93a26000 @
tcmalloc: large alloc 2175979520 bytes == 0x1160b6000 @
tcmalloc: large alloc 2339078144 bytes == 0x197fe3000 @
tcmalloc: large alloc 2339463168 bytes == 0x223b1b000 @
tcmalloc: large alloc 2341490688 bytes == 0x2af631000 @
tcmalloc: large alloc 2341588992 bytes == 0x33b3b6000 @
tcmalloc: large alloc 2341974016 bytes == 0x3c7153000 @
tcmalloc: large alloc 2461327360 bytes == 0xd137d3000 @
runMira_m07a.sh: line 521: 2659 Aborted mira --project=
$ASS -fasta --job=denovo,genome,454,sanger,accurate -OUT:ora=yes
-GE:not=4 -AS:urd=yes:klrs=no -SK:mmhr=5 454_SETTINGS
-CO:mrpg=8:mgqrt=30:mnq=20 > assembly_log.txt
The log looks like (pasting the header and the bottom):
This is MIRA V3.1.15 (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.
Mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
To (un-)subsubcribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
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
Wed Jun 2 20:35:52 CEST 2010
On: Linux arcadia64 2.6.27-11-generic #1 SMP Wed Apr 1 20:53:41 UTC 2009
x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compilation 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 q53.uppmax.uu.se 2.6.18-194.3.1.el5 #1 SMP Fri May
7 01:43:09 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=m07aNrPeM20 -fasta
--job=denovo,genome,454,sanger,accurate -OUT:ora=yes -GE:not=4
-AS:urd=yes:klrs=no -SK:mmhr=5 454_SETTINGS -CO:mrpg=8:mgqrt=30:mnq=20
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
Used parameter settings:
General (-GE):
Project name in (proin) : m07aNrPeM20
Project name out (proout) : m07aNrPeM20
Number of threads (not) : 4
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
Keep contigs in memory (kcim) : no
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[454] yes
Template insert size minimum (tismin) : [san] -1
[454] -1
Template insert size maximum (tismax) : [san] -1
[454] -1
Template partner build direction (tpbd) : [san] -1
[454] -1
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] yes
[454] yes
File type (ft) : [san] fasta
[454] fasta
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
Wants quality file (wqf) : [san] yes
[454] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[454] forward/reverse
(fr)
Merge with XML trace info (mxti) : [san] no
[454] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 5
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 3
Minimum read length (mrl) : [san] 80
[454] 40
Minimum reads per contig (mrpc) : [san] 2
[454] 5
Base default quality (bdq) : [san] 10
[454] 10
Enforce presence of qualities (epoq) : [san] yes
[454] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[454] 2
Minimum length (ardml) : [san] 400
[454] 200
Grace length (ardgl) : [san] 40
[454] 20
Use uniform read distribution (urd) : yes
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [san] 1.5
[454] 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
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) :
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
Read extension window length (rewl) : [san] 30
[454] 15
Read extension w. maxerrors (rewme) : [san] 2
[454] 2
First extension in pass (feip) : [san] 0
[454] 0
Last extension in pass (leip) : [san] 0
[454] 0
Clipping options (-CL):
Merge with SSAHA vector screen (msvs) : [san] no
[454] no
Gap size (msvsgs) : [san] 10
[454] 8
Max front gap (msvsmfg) : [san] 60
[454] 8
Max end gap (msvsmeg) : [san] 120
[454] 12
Strict front clip (msvssfc) : [san] 0
[454] 0
Strict end clip (msvssec) : [san] 0
[454] 0
Possible vector leftover clip (pvlc) : [san] yes
[454] no
maximum len allowed (pvcmla) : [san] 18
[454] 18
Quality clip (qc) : [san] no
[454] no
Minimum quality (qcmq) : [san] 20
[454] 20
Window length (qcwl) : [san] 30
[454] 30
Bad stretch quality clip (bsqc) : [san] yes
[454] no
Minimum quality (bsqcmq) : [san] 20
[454] 5
Window length (bsqcwl) : [san] 30
[454] 20
Masked bases clip (mbc) : [san] yes
[454] yes
Gap size (mbcgs) : [san] 20
[454] 5
Max front gap (mbcmfg) : [san] 40
[454] 12
Max end gap (mbcmeg) : [san] 60
[454] 12
Lower case clip (lcc) : [san] no
[454] yes
Clip poly A/T at ends (cpat) : [san] no
[454] no
Keep poly-a signal (cpkps) : [san] no
[454] no
Minimum signal length (cpmsl) : [san] 12
[454] 12
Max errors allowed (cpmea) : [san] 1
[454] 1
Max gap from ends (cpmgfe) : [san] 9
[454] 9
Ensure minimum left clip (emlc) : [san] yes
[454] no
Minimum left clip req. (mlcr) : [san] 25
[454] 4
Set minimum left clip to (smlc) : [san] 30
[454] 4
Ensure minimum right clip (emrc) : [san] no
[454] no
Minimum right clip req. (mrcr) : [san] 10
[454] 10
Set minimum right clip to (smrc) : [san] 20
[454] 15
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : yes
Bases per hash (pecbph) : 27
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 4
Bases per hash (bph) : 21
Hash save stepping (hss) : 1
Percent required (pr) : [san] 70
[454] 80
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 5
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
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[454] yes
Quick rule min len 1 (qrml1) : [san] 200
[454] 80
Quick rule min sim 1 (qrms1) : [san] 90
[454] 90
Quick rule min len 2 (qrml2) : [san] 100
[454] 60
Quick rule min sim 2 (qrms2) : [san] 95
[454] 95
Backbone quick overlap min len (bqoml) : [san] 150
[454] 80
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[454] 20
Bandwidth max (bmax) : [san] 130
[454] 80
Bandwidth min (bmin) : [san] 25
[454] 20
Minimum score (ms) : [san] 30
[454] 15
Minimum overlap (mo) : [san] 15
[454] 20
Minimum relative score in % (mrs) : [san] 70
[454] 70
Solexa_hack_max_errors (shme) : [san] 0
[454] 0
Extra gap penalty (egp) : [san] no
[454] yes
extra gap penalty level (egpl) : [san] low
[454] reject_codongaps
Max. egp in percent (megpp) : [san] 100
[454] 100
Contig parameters (-CO):
Name prefix (np) : m07aNrPeM20
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[454] 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] 8
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[454] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[454] 30
End-read Marking Exclusion Area in bases (emea) : [san] 1
[454] 10
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[454] no
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[454] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[454] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[454] no
Merge short reads (msr) : [san] no
[454] no
Gap override ratio (gor) : [san] 66
[454] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[454] yes
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Directories (-DI):
When loading EXP files :
When loading SCF files :
Top directory for writing files : m07aNrPeM20_assembly
For writing result files :
m07aNrPeM20_assembly/m07aNrPeM20_d_results
For writing result info files :
m07aNrPeM20_assembly/m07aNrPeM20_d_info
For writing log files :
m07aNrPeM20_assembly/m07aNrPeM20_d_log
For writing checkpoint files :
m07aNrPeM20_assembly/m07aNrPeM20_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
m07aNrPeM20_in.sanger.fasta
[454]
m07aNrPeM20_in.454.fasta
When loading qualities from FASTA quality : [san]
m07aNrPeM20_in.sanger.fasta.qual
[454]
m07aNrPeM20_in.454.fasta.qual
When loading sequences from FASTQ : [san]
m07aNrPeM20_in.sanger.fastq
[454]
m07aNrPeM20_in.454.fastq
When loading project from CAF :
m07aNrPeM20_in.sanger.caf
When loading project from MAF (disabled) :
m07aNrPeM20_in.sanger.maf
When loading EXP fofn :
m07aNrPeM20_in.sanger.fofn
When loading project from PHD : m07aNrPeM20_in.phd.1
When loading strain data :
m07aNrPeM20_straindata_in.txt
When loading XML trace info files : [san]
m07aNrPeM20_traceinfo_in.sanger.xml
[454]
m07aNrPeM20_traceinfo_in.454.xml
When loading SSAHA vector screen results :
m07aNrPeM20_ssaha2vectorscreen_in.txt
When loading backbone from MAF :
m07aNrPeM20_backbone_in.maf
When loading backbone from CAF :
m07aNrPeM20_backbone_in.caf
When loading backbone from GenBank :
m07aNrPeM20_backbone_in.gbf
When loading backbone from FASTA :
m07aNrPeM20_backbone_in.fasta
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[454] no
Save tagged singlets in project (stsip) : [san] yes
[454] yes
Remove rollover logs (rrol) : yes
Remove log directory (rld) : no
Result files:
Saved as CAF (orc) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : yes
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 : m07aNrPeM20_out.caf
MAF : m07aNrPeM20_out.maf
FASTA : m07aNrPeM20_out.unpadded.fasta
FASTA quality : m07aNrPeM20_out.unpadded.fasta.qual
FASTA (padded) : m07aNrPeM20_out.padded.fasta
FASTA qual.(pad): m07aNrPeM20_out.padded.fasta.qual
GAP4 (directory): m07aNrPeM20_out.gap4da
ACE : m07aNrPeM20_out.ace
HTML : m07aNrPeM20_out.html
Simple text : m07aNrPeM20_out.txt
TCS overview : m07aNrPeM20_out.tcs
Wiggle : m07aNrPeM20_out.wig
------------------------------------------------------------------------------
Creating directory m07aNrPeM20_assembly ... done.
Creating directory m07aNrPeM20_assembly/m07aNrPeM20_d_log ... done.
Creating directory m07aNrPeM20_assembly/m07aNrPeM20_d_results ... done.
Creating directory m07aNrPeM20_assembly/m07aNrPeM20_d_info ... done.
Creating directory m07aNrPeM20_assembly/m07aNrPeM20_d_chkpt ... done.
Localtime: Wed Jun 30 17:59:50 2010
[...]
[48758] +pa+++ap++paa++++apaappp+++++a++p+pppaaappppppp+pp+aa+++a+pp
335640 14514 / 1071596 / 15826
Ouch, out of memory detected.
========================== Memory self assessment
==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 24676992 kB
MemFree: 95292 kB
Buffers: 932 kB
Cached: 19932 kB
SwapCached: 382096 kB
Active: 10795872 kB
Inactive: 13165256 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 24676992 kB
LowFree: 95292 kB
SwapTotal: 26732152 kB
SwapFree: 1715328 kB
Dirty: 4 kB
Writeback: 100 kB
AnonPages: 23711460 kB
Mapped: 9244 kB
Slab: 58024 kB
PageTables: 384444 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 39070648 kB
Committed_AS: 195407984 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 24608 kB
VmallocChunk: 34359689427 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 78%
Tgid: 2659
Pid: 2659
PPid: 2647
TracerPid: 0
Uid: 40970 40970 40970 40970
Gid: 40001 40001 40001 40001
FDSize: 256
Groups: 40001 2009043
VmPeak: 195297200 kB
VmSize: 195297200 kB
VmLck: 0 kB
VmHWM: 24082080 kB
VmRSS: 23707436 kB
VmData: 195289740 kB
VmStk: 2932 kB
VmExe: 4492 kB
VmLib: 0 kB
VmPTE: 381456 kB
StaBrk: 1bce8000 kB
Brk: 2eaad26000 kB
StaStk: 7fffbe959af0 kB
Threads: 1
SigQ: 0/204800
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000001000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,0000ffff
Mems_allowed: 00000000,00000003
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 332471 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1091643808 (1.0 GiB)
Memory used in assembly structures:
Eff. Size Free cap.
LostByAlign
AS_writtenskimhitsperid: 332471 1 MiB 0 B
4 B
AS_skim_edges: 0 24 B 0 B
0 B
AS_adsfacts: 7425021 157 MiB 16 MiB
4 B
AS_confirmed_edges: 14850040 314 MiB 31 MiB
4 B
AS_permanent_overlap_bans: 6919864 279 MiB 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: 332471 1 MiB 0 B
4 B
AS_clipright: 332471 1 MiB 0 B
4 B
AS_used_ids: 332471 325 KiB 0 B
1 B
AS_multicopies: 332471 325 KiB 0 B
1 B
AS_hasmcoverlaps: 0 325 KiB 325 KiB
1 B
AS_maxcoveragereached: 332471 1 MiB 0 B
4 B
AS_coverageperseqtype: 0 24 B 0 B
0 B
AS_istroublemaker: 332471 325 KiB 0 B
1 B
AS_isdebris: 332471 325 KiB 0 B
1 B
AS_needalloverlaps: 332471 325 KiB 9 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: 36 1 KiB 0 B
0 B
Total: 1886020664 (1.8 GiB)
================================================================================
========================== Memory self assessment
==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 24676992 kB
MemFree: 89228 kB
Buffers: 292 kB
Cached: 9688 kB
SwapCached: 437236 kB
Active: 23120048 kB
Inactive: 846464 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 24676992 kB
LowFree: 89228 kB
SwapTotal: 26732152 kB
SwapFree: 1676156 kB
Dirty: 8 kB
Writeback: 0 kB
AnonPages: 23690196 kB
Mapped: 9488 kB
Slab: 58648 kB
PageTables: 384444 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 39070648 kB
Committed_AS: 195407984 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 24608 kB
VmallocChunk: 34359689427 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 78%
Tgid: 2659
Pid: 2659
PPid: 2647
TracerPid: 0
Uid: 40970 40970 40970 40970
Gid: 40001 40001 40001 40001
FDSize: 256
Groups: 40001 2009043
VmPeak: 195297200 kB
VmSize: 195297200 kB
VmLck: 0 kB
VmHWM: 24082080 kB
VmRSS: 23686232 kB
VmData: 195289740 kB
VmStk: 2932 kB
VmExe: 4492 kB
VmLib: 0 kB
VmPTE: 381456 kB
StaBrk: 1bce8000 kB
Brk: 2eaad26000 kB
StaStk: 7fffbe959af0 kB
Threads: 1
SigQ: 0/204800
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000001000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,0000ffff
Mems_allowed: 00000000,00000003
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 332471 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 1091643808 (1.0 GiB)
Memory used in assembly structures:
Eff. Size Free cap.
LostByAlign
AS_writtenskimhitsperid: 332471 1 MiB 0 B
4 B
AS_skim_edges: 0 24 B 0 B
0 B
AS_adsfacts: 7425021 157 MiB 16 MiB
4 B
AS_confirmed_edges: 14850040 314 MiB 31 MiB
4 B
AS_permanent_overlap_bans: 6919864 279 MiB 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: 332471 1 MiB 0 B
4 B
AS_clipright: 332471 1 MiB 0 B
4 B
AS_used_ids: 332471 325 KiB 0 B
1 B
AS_multicopies: 332471 325 KiB 0 B
1 B
AS_hasmcoverlaps: 0 325 KiB 325 KiB
1 B
AS_maxcoveragereached: 332471 1 MiB 0 B
4 B
AS_coverageperseqtype: 0 24 B 0 B
0 B
AS_istroublemaker: 332471 325 KiB 0 B
1 B
AS_isdebris: 332471 325 KiB 0 B
1 B
AS_needalloverlaps: 332471 325 KiB 9 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: 36 1 KiB 0 B
0 B
Total: 1886020664 (1.8 GiB)
================================================================================
Dynamic allocs: 2443
Align allocs: 1836
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.
Any idea what could have happened? I'm now trying to run it again with
-GE:amm=0, any guess if it might help?
Best,
Lionel
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