I would say you ran out of memory... How much system RAM do you have available? Francisco On 18/11/13 11:15, Amit Bikram wrote:
Hi. i have used this commandmira --project=isab --job=denovo,genome,accurate,454 --fasta=isab_in.454.fa 454_SETTINGS -LR:wqf=no > log.txtand i am getting this error This is MIRA V3.4.1.1 (production version).Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome SequenceAssembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. To (un-)subscribe the MIRA mailing lists, see: http://www.chevreux.org/mira_mailinglists.html After subscribing, mail general questions to the MIRA talk mailing list: mira_talk@xxxxxxxxxxxxx <mailto:mira_talk@xxxxxxxxxxxxx>To report bugs or ask for features, please use the new ticketing system at:http://sourceforge.net/apps/trac/mira-assembler/ This ensures that requests don't get lost. Compiled by: bach Wed Nov 14 23:07:20 CET 2012On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012 x86_64 GNU/LinuxCompiled 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: 8Current system: Linux orf-desktop 3.8.0-32-generic #47-Ubuntu SMP Tue Oct 1 22:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/LinuxParsing parameters: --project=isab --job=denovo,genome,accurate,454 --fasta=isab_in.454.fa 454_SETTINGS -LR:wqf=noParameters 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) : isab Project name out (proout) : isab Number of threads (not) : 2 Automatic memory management (amm) : yes Keep percent memory free (kpmf) : 15 Max. process size (mps) : 0 EST SNP pipeline step (esps) : 0 Use template information (uti) : [san] yes [454] yes 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] 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) : no FASTQ qual offset (fqqo) : [san] 0 [454] 0 Wants quality file (wqf) : [san] yes [454] noRead 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 Maximum contigs per pass (mcpp) : 0 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) : no 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 Assign default strain (ads) : [san] no [454] no Default strain name (dsn) : [san] StrainX [454] StrainX Load backbone (lb) : no Start backbone usage in pass (sbuip) : 3 Backbone file type (bft) : fasta Backbone base quality (bbq) : 30 Backbone strain name (bsn) : ReferenceStrain Force for all (bsnffa) : no Backbone rail from strain (brfs) : Backbone rail length (brl) : 0 Backbone rail overlap (bro) : 0 Also build new contigs (abnc) : yes Dataprocessing options (-DP): Use read extensions (ure) : [san] yes [454] no 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 SSAHA2/SMALT 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 Min qual. threshold for entire read (mqtfer): [san] 0 [454] 0 Number of bases (mqtfernob) : [san] 0 [454] 0 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 Clip 3 prime polybase (c3pp) : [san] no [454] no Minimum signal length (c3ppmsl) : [san] 12 [454] 12 Max errors allowed (c3ppmea) : [san] 2 [454] 2 Max gap from ends (c3ppmgfe) : [san] 9 [454] 9 Clip known adaptors right (ckar) : [san] no [454] yes 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 Handle Solexa GGCxG problem (pechsgp) : yes Clip bad solexa ends (cbse) : yes Parameters for SKIM algorithm (-SK): Number of threads (not) : 2 Also compute reverse complements (acrc) : yes 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) : 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) : 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 Max. start cache fill time (mscft) : 5 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] 17 [454] 20 Minimum relative score in % (mrs) : [san] 70 [454] 70 Solexa_hack_max_errors (shme) : [san] -1 [454] -1 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) : isab 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] 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] 1 [454] 1 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 Keep ends unmerged (msrkeu) : [san] -1 [454] -1 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 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 : isab_assembly For writing result files : isab_assembly/isab_d_results For writing result info files : isab_assembly/isab_d_info For writing tmp files : isab_assembly/isab_d_tmp Tmp redirected to (trt) : For writing checkpoint files : isab_assembly/isab_d_chkpt File names (-FN): When loading sequences from FASTA : [san] isab_in.454.fa [454] isab_in.454.faWhen loading qualities from FASTA quality : [san] isab_in.454.fa.qual [454] isab_in.454.fa.qual When loading sequences from FASTQ : [san] isab_in.sanger.fastq [454] isab_in.454.fastqWhen loading project from CAF : isab_in.sanger.caf When loading project from MAF (disabled) : isab_in.sanger.maf When loading EXP fofn : isab_in.sanger.fofn When loading project from PHD : isab_in.phd.1 When loading strain data : isab_straindata_in.txtWhen loading XML trace info files : [san] isab_traceinfo_in.sanger.xml [454] isab_traceinfo_in.454.xml When loading SSAHA2 vector screen results : isab_ssaha2vectorscreen_in.txt When loading SMALT vector screen results : isab_smaltvectorscreen_in.txtWhen loading backbone from MAF : isab_backbone_in.maf When loading backbone from CAF : isab_backbone_in.caf When loading backbone from GenBank : isab_backbone_in.gbf When loading backbone from GFF3 : isab_backbone_in.gff3 When loading backbone from FASTA : isab_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 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 : isab_out.caf MAF : isab_out.maf FASTA : isab_out.unpadded.fasta FASTA quality : isab_out.unpadded.fasta.qual FASTA (padded) : isab_out.padded.fasta FASTA qual.(pad): isab_out.padded.fasta.qual GAP4 (directory): isab_out.gap4da ACE : isab_out.ace HTML : isab_out.html Simple text : isab_out.txt TCS overview : isab_out.tcs Wiggle : isab_out.wig ------------------------------------------------------------------------------ Creating directory isab_assembly ... done. Creating directory isab_assembly/isab_d_tmp ... done. Creating directory isab_assembly/isab_d_results ... done. Creating directory isab_assembly/isab_d_info ... done. Creating directory isab_assembly/isab_d_chkpt ... done. Tmp directory is not on a NFS mount, good. Localtime: Mon Nov 18 14:30:46 2013 Loading data (454) from FASTA files,Could not find FASTA quality file isab_in.454.fa.qual, using default values for these reads.Localtime: Mon Nov 18 14:30:46 2013 Counting sequences in FASTA file:[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]Found 4758954 sequences. Localtime: Mon Nov 18 14:31:15 2013 454 will load 4758954 reads. Longest Sanger: 0 Longest 454: 1196 Longest IonTor: 0 Longest PacBio: 0 Longest Solexa: 0 Longest Solid: 0 Longest overall: 1196 Total reads to load: 4758954 Reserving space for reads (this may take a while) Reserved space for 4758964 reads. Loading data (454) from FASTA files,Could not find FASTA quality file isab_in.454.fa.qual, using default values for these reads.Localtime: Mon Nov 18 14:31:15 2013 Localtime: Mon Nov 18 14:31:15 2013 Loading data from FASTA file:[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|...this is in log file and in command line it shows KILLED please help me to find out the error with regards Amit