Hi, I am trying to use mira for a de novo assembly of a transcriptome but after running for a few minutes, it gives me a memory related error. Writing temporary hstat files: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done Analysing hstat files: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Ouch, out of memory detected. My data is from 454 GS FLX Titanium series and I have nearly 650,000 reads with associated quality file. I am using a strong server with 32 gb RAM. Any idea why this might be happening? I am using the following command to run mira: mira -project=1TCA --job=denovo,est,normal,454 -fasta -notraceinfo -noclipping >&log_assembly.txt Also I am unable to figure out how to invoke the miraMEM memory call. When I try giving this as command, my shell returns with command not found and mira doesn't seem to accept is as an option or argument. Can you tell me what linux command should I give to invoke miraMEM to get an estimate of how much memory my project might need ? I am attaching the log assembly results for convenience Thanks Ankit Gupta Graduate Student at Virginia Tech
This is MIRA V3rc4 (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 in 32 bit mode. Compiled in boundtracking mode. Compiled in bugtracking mode. Parsing parameters: -project=1TCA --job=denovo,est,normal,454 -fasta -notraceinfo -noclipping Using quickmode switch -notraceinfo : SANGER_SETTINGS -LR:mxti=no 454_SETTINGS -LR:mxti=no SOLEXA_SETTINGS -LR:mxti=no SOLID_SETTINGS -LR:mxti=no Using quickmode switch -noclipping : SANGER_SETTINGS -CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no 454_SETTINGS -CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no SOLEXA_SETTINGS -CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no SOLID_SETTINGS -CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no Parameters parsed without error, perfect. ------------------------------------------------------------------------------ Parameter settings seen for: Sanger data (also common parameters), 454 data Used parameter settings: General (-GE): Project name in (proin) : 1TCA Project name out (proout) : 1TCA Number of threads (not) : 2 Automatic memory management (amm) : yes Keep percent memory free (kpmf) : 10 Max. process size (mps) : 0 Keep contigs in memory (kcim) : no EST SNP pipeline step (esps) : 1 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 Colour reads by hash frequency (crhf) : no Load reads options (-LR): Load sequence data (lsd) : [san] no [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) : yes 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] no Filecheck only (fo) : no Assembly options (-AS): Number of passes (nop) : 4 Skim each pass (sep) : yes Maximum number of RMB break loops (rbl) : 2 Minimum read length (mrl) : [san] 80 [454] 40 Base default quality (bdq) : [san] 10 [454] 10 Enforce presence of qualities (epoq) : [san] yes [454] yes Automatic repeat detection (ard) : no 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) : no Start in pass (urdsip) : 3 Cutoff multiplier (urdcm) : [san] 1.5 [454] 1.5 Keep long repeats separated (klrs) : no Spoiler detection (sd) : no Last pass only (sdlpo) : yes Use genomic pathfinder (ugpf) : no Use emergency search stop (uess) : yes ESS partner depth (esspd) : 500 Use emergency blacklist (uebl) : yes Use max. contig build time (umcbt) : yes Build time in seconds (bts) : 3600 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] no [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] 30 [454] 8 Max end gap (msvsmeg) : [san] 60 [454] 12 Strict front clip (msvssfc) : [san] 0 [454] 0 Strict end clip (msvssec) : [san] 0 [454] 0 Possible vector leftover clip (pvlc) : [san] no [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] no [454] no Minimum quality (bsqcmq) : [san] 20 [454] 5 Window length (bsqcwl) : [san] 30 [454] 20 Masked bases clip (mbc) : [san] no [454] no 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 (llc) : [san] no [454] no 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] 20000 [454] 20000 Ensure minimum left clip (emlc) : [san] no [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 Propose end clips (pec) : no Bases per hash (pecbph) : 0 Parameters for SKIM algorithm (-SK): Number of threads (not) : 2 Bases per hash (bph) : 17 Hash save stepping (hss) : 4 Percent required (pr) : [san] 70 [454] 80 Max hits per read (mhpr) : 30 Mask nasty repeats (mnr) : no Nasty repeat ratio (nrr) : 100 Max. megahub ratio (mmhr) : 0 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] 15 [454] 20 Bandwidth max (bmax) : [san] 100 [454] 80 Bandwidth min (bmin) : [san] 25 [454] 20 Minimum score (ms) : [san] 30 [454] 15 Minimum overlap (mo) : [san] 15 [454] 40 Minimum relative score in % (mrs) : [san] 80 [454] 80 Solexa_hack_max_errors (shme) : [san] 0 [454] 0 Extra gap penalty (egp) : [san] yes [454] yes extra gap penalty level (egpl) : [san] reject_codongaps [454] reject_codongaps Max. egp in percent (megpp) : [san] 100 [454] 100 Contig parameters (-CO): Name prefix (np) : 1TCA Reject on drop in relative alignment score in % (rodirs) : [san] 20 [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] 4 Minimum neighbour quality needed for tagging (mnq) : [san] 20 [454] 20 Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30 [454] 25 End-read Marking Exclusion Area in bases (emea) : [san] 25 [454] 10 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 : For writing result files : 1TCA_d_results For writing result info files : 1TCA_d_info For writing log files : 1TCA_d_log For writing checkpoint files : 1TCA_d_chkpt File names (-FN): When loading sequences from FASTA : [san] 1TCA_in.sanger.fasta [454] 1TCA_in.454.fasta When loading qualities from FASTA quality : [san] 1TCA_in.sanger.fasta.qual [454] 1TCA_in.454.fasta.qual When loading sequences from FASTQ : [san] 1TCA_in.sanger.fastq [454] 1TCA_in.454.fastq When loading project from CAF : 1TCA_in.sanger.caf When loading project from MAF (disabled) : 1TCA_in.sanger.maf When loading EXP fofn : 1TCA_in.fofn When loading project from PHD : 1TCA_in.phd.1 When loading strain data : 1TCA_straindata_in.txt When loading XML trace info files : [san] 1TCA_traceinfo_in.sanger.xml [454] 1TCA_traceinfo_in.454.xml When loading SSAHA vector screen results : 1TCA_ssahavectorscreen_in.txt When loading backbone from CAF : 1TCA_backbone_in.caf When loading backbone from GenBank : 1TCA_backbone_in.gbf When loading backbone from FASTA : 1TCA_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) : no Temporary result files: Saved as CAF (otc) : yes Saved as CAF (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 : 1TCA_out.caf MAF : 1TCA_out.maf FASTA : 1TCA_out.unpadded.fasta FASTA quality : 1TCA_out.unpadded.fasta.qual FASTA (padded) : 1TCA_out.padded.fasta FASTA qual.(pad): 1TCA_out.padded.fasta.qual GAP4 (directory): 1TCA_out.gap4da ACE : 1TCA_out.ace HTML : 1TCA_out.html Simple text : 1TCA_out.txt TCS overview : 1TCA_out.tcs Wiggle : 1TCA_out.wig ------------------------------------------------------------------------------ Deleting old directory 1TCA_d_log ... done. Creating directory 1TCA_d_log ... done. Deleting old directory 1TCA_d_results ... done. Creating directory 1TCA_d_results ... done. Deleting old directory 1TCA_d_info ... done. Creating directory 1TCA_d_info ... done. Deleting old directory 1TCA_d_chkpt ... done. Creating directory 1TCA_d_chkpt ... done. Localtime: Thu Dec 3 13:42:15 2009 Loading data (454) from FASTA files, Counting sequences in FASTA file: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Found 636034 sequences. 454 will load 636034 reads. Longest Sanger: 0 Longest 454: 644 Longest Solexa: 0 Longest Solid: 0 Longest overall: 644 Total reads to load: 636034 Reserving space for reads (this may take a while) Reserved space for 636044 reads. Loading data (454) from FASTA files, Counting sequences in FASTA file: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Found 636034 sequences. Loading data from FASTA file: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Loading quality data from FASTA quality file 1TCA_in.454.fasta.qual: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Done. Loaded 636034 reads, 636034 of which have quality accounted for. Loaded 636034 454 reads. Total reads loaded: 636034 ========================== Memory self assessment ============================== Running in 64 bit mode. Dump from /proc/meminfo -------------------------------------------------------------------------------- MemTotal: 32429216 kB MemFree: 21445252 kB Buffers: 776 kB Cached: 8252344 kB SwapCached: 0 kB Active: 7261480 kB Inactive: 3360724 kB HighTotal: 31815552 kB HighFree: 21350704 kB LowTotal: 613664 kB LowFree: 94548 kB SwapTotal: 8388600 kB SwapFree: 8388600 kB Dirty: 1164 kB Writeback: 0 kB AnonPages: 2368792 kB Mapped: 18796 kB Slab: 334864 kB SReclaimable: 321968 kB SUnreclaim: 12896 kB PageTables: 5820 kB NFS_Unstable: 0 kB Bounce: 0 kB WritebackTmp: 0 kB CommitLimit: 24603208 kB Committed_AS: 2434328 kB VmallocTotal: 110584 kB VmallocUsed: 9968 kB VmallocChunk: 83808 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 HugePages_Surp: 0 Hugepagesize: 2048 kB DirectMap4k: 6144 kB DirectMap2M: 911360 kB -------------------------------------------------------------------------------- Dump from /proc/self/status -------------------------------------------------------------------------------- Name: mira State: R (running) Tgid: 10488 Pid: 10488 PPid: 4454 TracerPid: 0 Uid: 20634 20634 20634 20634 Gid: 100 100 100 100 FDSize: 256 Groups: 100 VmPeak: 2339020 kB VmSize: 2325936 kB VmLck: 0 kB VmHWM: 2334968 kB VmRSS: 2322008 kB VmData: 2320044 kB VmStk: 84 kB VmExe: 2648 kB VmLib: 3024 kB VmPTE: 4552 kB Threads: 1 SigQ: 0/262144 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000000000000 SigCgt: 0000000180000000 CapInh: 0000000000000000 CapPrm: 0000000000000000 CapEff: 0000000000000000 CapBnd: ffffffffffffffff Cpus_allowed: 00000000,00000000,00000000,000000ff Cpus_allowed_list: 0-7 Mems_allowed: 01 Mems_allowed_list: 0 voluntary_ctxt_switches: 9 nonvoluntary_ctxt_switches: 178 -------------------------------------------------------------------------------- Information on current assembly object: AS_readpool: 636034 reads. AS_contigs: 0 contigs. AS_bbcontigs: 0 contigs. Mem used for reads: 2355002064 (2.2 GiB) Memory used in assembly structures: Eff. Size Free cap. LostByAlign AS_writtenskimhitsperid: 0 12 B 0 B 0 B AS_skim_edges: 0 12 B 0 B 0 B AS_adsfacts: 0 12 B 0 B 0 B AS_confirmed_edges: 0 12 B 0 B 0 B AS_permanent_overlap_bans: 0 12 B 0 B 0 B AS_readhitmiss: 0 12 B 0 B 0 B AS_readhmcovered: 0 12 B 0 B 0 B AS_count_rhm: 0 12 B 0 B 0 B AS_clipleft: 0 12 B 0 B 0 B AS_clipright: 0 12 B 0 B 0 B AS_used_ids: 0 12 B 0 B 0 B AS_multicopies: 0 12 B 0 B 0 B AS_hasmcoverlaps: 0 12 B 0 B 0 B AS_maxcoveragereached: 0 12 B 0 B 0 B AS_coverageperseqtype: 0 12 B 0 B 0 B AS_istroublemaker: 0 12 B 0 B 0 B AS_isdebris: 0 12 B 0 B 0 B AS_needalloverlaps: 0 20 B 0 B 0 B AS_readsforrepeatresolve: 0 20 B 0 B 0 B AS_allrmbsok: 0 12 B 0 B 0 B AS_probablermbsnotok: 0 12 B 0 B 0 B AS_weakrmbsnotok: 0 12 B 0 B 0 B AS_readmaytakeskim: 0 20 B 0 B 0 B AS_skimstaken: 0 20 B 0 B 0 B AS_numskimoverlaps: 0 12 B 0 B 0 B AS_numleftextendskims: 0 12 B 0 B 0 B AS_rightextendskims: 0 12 B 0 B 0 B AS_skimleftextendratio: 0 12 B 0 B 0 B AS_skimrightextendratio: 0 12 B 0 B 0 B AS_usedlogfiles: 1 24 B 0 B 0 B Total: 2355002468 (2.2 GiB) ================================================================================ 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. 636034 reads with valid data for assembly. Localtime: Thu Dec 3 13:45:14 2009 Generated 636034 unique template ids for 636034 valid reads. No useful template information found, template routines will not be used. Localtime: Thu Dec 3 13:45:26 2009 Generated 0 unique strain ids for 636034 reads. Strain "default" has 636034 reads. Have read pool with 636034 reads. =========================================================================== Pool statistics: Backbones: 0 Backbone rails: 0 Sanger 454 Solexa SOLiD --------------------------------- Total reads 0 636034 0 0 Reads wo qual 0 0 0 0 Used reads 0 636034 0 0 Avg len used 0 387 0 0 With strain 0 0 0 0 W/o clips 0 636034 0 0 =========================================================================== =========================================================================== Pool statistics: Backbones: 0 Backbone rails: 0 Sanger 454 Solexa SOLiD --------------------------------- Total reads 0 636034 0 0 Reads wo qual 0 0 0 0 Used reads 0 636034 0 0 Avg len used 0 387 0 0 With strain 0 0 0 0 W/o clips 0 636034 0 0 =========================================================================== Writing temporary hstat files: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done Analysing hstat files: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Ouch, out of memory detected. ========================== Memory self assessment ============================== Running in 64 bit mode. Dump from /proc/meminfo -------------------------------------------------------------------------------- MemTotal: 32429216 kB MemFree: 14659912 kB Buffers: 776 kB Cached: 14926184 kB SwapCached: 0 kB Active: 7289080 kB Inactive: 10034884 kB HighTotal: 31815552 kB HighFree: 14648824 kB LowTotal: 613664 kB LowFree: 11088 kB SwapTotal: 8388600 kB SwapFree: 8388600 kB Dirty: 43304 kB Writeback: 8176 kB AnonPages: 2396220 kB Mapped: 19448 kB Slab: 418832 kB SReclaimable: 405444 kB SUnreclaim: 13388 kB PageTables: 5764 kB NFS_Unstable: 0 kB Bounce: 0 kB WritebackTmp: 0 kB CommitLimit: 24603208 kB Committed_AS: 2466592 kB VmallocTotal: 110584 kB VmallocUsed: 9968 kB VmallocChunk: 83808 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 HugePages_Surp: 0 Hugepagesize: 2048 kB DirectMap4k: 6144 kB DirectMap2M: 911360 kB -------------------------------------------------------------------------------- Dump from /proc/self/status -------------------------------------------------------------------------------- Name: mira State: R (running) Tgid: 10488 Pid: 10488 PPid: 4454 TracerPid: 0 Uid: 20634 20634 20634 20634 Gid: 100 100 100 100 FDSize: 256 Groups: 100 VmPeak: 2752996 kB VmSize: 2359972 kB VmLck: 0 kB VmHWM: 2741832 kB VmRSS: 2347900 kB VmData: 2354080 kB VmStk: 84 kB VmExe: 2648 kB VmLib: 3024 kB VmPTE: 4620 kB Threads: 1 SigQ: 0/262144 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000000000000 SigCgt: 0000000180000000 CapInh: 0000000000000000 CapPrm: 0000000000000000 CapEff: 0000000000000000 CapBnd: ffffffffffffffff Cpus_allowed: 00000000,00000000,00000000,000000ff Cpus_allowed_list: 0-7 Mems_allowed: 01 Mems_allowed_list: 0 voluntary_ctxt_switches: 1574 nonvoluntary_ctxt_switches: 11828 -------------------------------------------------------------------------------- Information on current assembly object: AS_readpool: 636034 reads. AS_contigs: 0 contigs. AS_bbcontigs: 0 contigs. Mem used for reads: 2355002064 (2.2 GiB) Memory used in assembly structures: Eff. Size Free cap. LostByAlign AS_writtenskimhitsperid: 0 12 B 0 B 0 B AS_skim_edges: 0 12 B 0 B 0 B AS_adsfacts: 0 12 B 0 B 0 B AS_confirmed_edges: 0 12 B 0 B 0 B AS_permanent_overlap_bans: 0 15 MiB 0 B 0 B AS_readhitmiss: 0 12 B 0 B 0 B AS_readhmcovered: 0 12 B 0 B 0 B AS_count_rhm: 0 12 B 0 B 0 B AS_clipleft: 636034 2 MiB 0 B 0 B AS_clipright: 636034 2 MiB 0 B 0 B AS_used_ids: 636034 621 KiB 0 B 2 B AS_multicopies: 0 621 KiB 621 KiB 2 B AS_hasmcoverlaps: 0 621 KiB 621 KiB 2 B AS_maxcoveragereached: 636034 2 MiB 0 B 0 B AS_coverageperseqtype: 0 12 B 0 B 0 B AS_istroublemaker: 636034 621 KiB 0 B 2 B AS_isdebris: 636034 621 KiB 0 B 2 B AS_needalloverlaps: 636034 621 KiB 30 B 0 B AS_readsforrepeatresolve: 0 20 B 0 B 0 B AS_allrmbsok: 0 2 MiB 2 MiB 0 B AS_probablermbsnotok: 0 2 MiB 2 MiB 0 B AS_weakrmbsnotok: 0 2 MiB 2 MiB 0 B AS_readmaytakeskim: 0 20 B 0 B 0 B AS_skimstaken: 0 20 B 0 B 0 B AS_numskimoverlaps: 0 12 B 0 B 0 B AS_numleftextendskims: 0 12 B 0 B 0 B AS_rightextendskims: 0 12 B 0 B 0 B AS_skimleftextendratio: 0 12 B 0 B 0 B AS_skimrightextendratio: 0 12 B 0 B 0 B AS_usedlogfiles: 2 40 B 0 B 0 B Total: 2389348360 (2.2 GiB) ================================================================================ ========================== Memory self assessment ============================== Running in 64 bit mode. Dump from /proc/meminfo -------------------------------------------------------------------------------- MemTotal: 32429216 kB MemFree: 14590624 kB Buffers: 776 kB Cached: 14926300 kB SwapCached: 0 kB Active: 7358064 kB Inactive: 10034604 kB HighTotal: 31815552 kB HighFree: 14579528 kB LowTotal: 613664 kB LowFree: 11096 kB SwapTotal: 8388600 kB SwapFree: 8388600 kB Dirty: 43212 kB Writeback: 8272 kB AnonPages: 2465640 kB Mapped: 20384 kB Slab: 418844 kB SReclaimable: 405444 kB SUnreclaim: 13400 kB PageTables: 5832 kB NFS_Unstable: 0 kB Bounce: 0 kB WritebackTmp: 0 kB CommitLimit: 24603208 kB Committed_AS: 2548100 kB VmallocTotal: 110584 kB VmallocUsed: 9968 kB VmallocChunk: 83808 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 HugePages_Surp: 0 Hugepagesize: 2048 kB DirectMap4k: 6144 kB DirectMap2M: 911360 kB -------------------------------------------------------------------------------- Dump from /proc/self/status -------------------------------------------------------------------------------- Name: mira State: R (running) Tgid: 10488 Pid: 10488 PPid: 4454 TracerPid: 0 Uid: 20634 20634 20634 20634 Gid: 100 100 100 100 FDSize: 256 Groups: 100 VmPeak: 2752996 kB VmSize: 2359972 kB VmLck: 0 kB VmHWM: 2741832 kB VmRSS: 2347900 kB VmData: 2354080 kB VmStk: 84 kB VmExe: 2648 kB VmLib: 3024 kB VmPTE: 4620 kB Threads: 1 SigQ: 0/262144 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000000000000 SigCgt: 0000000180000000 CapInh: 0000000000000000 CapPrm: 0000000000000000 CapEff: 0000000000000000 CapBnd: ffffffffffffffff Cpus_allowed: 00000000,00000000,00000000,000000ff Cpus_allowed_list: 0-7 Mems_allowed: 01 Mems_allowed_list: 0 voluntary_ctxt_switches: 1574 nonvoluntary_ctxt_switches: 11829 -------------------------------------------------------------------------------- Information on current assembly object: AS_readpool: 636034 reads. AS_contigs: 0 contigs. AS_bbcontigs: 0 contigs. Mem used for reads: 2355002064 (2.2 GiB) Memory used in assembly structures: Eff. Size Free cap. LostByAlign AS_writtenskimhitsperid: 0 12 B 0 B 0 B AS_skim_edges: 0 12 B 0 B 0 B AS_adsfacts: 0 12 B 0 B 0 B AS_confirmed_edges: 0 12 B 0 B 0 B AS_permanent_overlap_bans: 0 15 MiB 0 B 0 B AS_readhitmiss: 0 12 B 0 B 0 B AS_readhmcovered: 0 12 B 0 B 0 B AS_count_rhm: 0 12 B 0 B 0 B AS_clipleft: 636034 2 MiB 0 B 0 B AS_clipright: 636034 2 MiB 0 B 0 B AS_used_ids: 636034 621 KiB 0 B 2 B AS_multicopies: 0 621 KiB 621 KiB 2 B AS_hasmcoverlaps: 0 621 KiB 621 KiB 2 B AS_maxcoveragereached: 636034 2 MiB 0 B 0 B AS_coverageperseqtype: 0 12 B 0 B 0 B AS_istroublemaker: 636034 621 KiB 0 B 2 B AS_isdebris: 636034 621 KiB 0 B 2 B AS_needalloverlaps: 636034 621 KiB 30 B 0 B AS_readsforrepeatresolve: 0 20 B 0 B 0 B AS_allrmbsok: 0 2 MiB 2 MiB 0 B AS_probablermbsnotok: 0 2 MiB 2 MiB 0 B AS_weakrmbsnotok: 0 2 MiB 2 MiB 0 B AS_readmaytakeskim: 0 20 B 0 B 0 B AS_skimstaken: 0 20 B 0 B 0 B AS_numskimoverlaps: 0 12 B 0 B 0 B AS_numleftextendskims: 0 12 B 0 B 0 B AS_rightextendskims: 0 12 B 0 B 0 B AS_skimleftextendratio: 0 12 B 0 B 0 B AS_skimrightextendratio: 0 12 B 0 B 0 B AS_usedlogfiles: 2 40 B 0 B 0 B Total: 2389348360 (2.2 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 (or better, the complete log) of the output log 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.