[mira_talk] Re: problem in denovo assembly fasta file
- From: Amit Bikram <amitbikram87@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 18 Nov 2013 19:29:52 +0530
I have 16gb RAM
with regards
Amit
On Mon, Nov 18, 2013 at 4:51 PM, Francisco Pina Martins <
f.pinamartins@xxxxxxxxx> wrote:
> 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 command
> mira --project=isab --job=denovo,genome,accurate,454
> --fasta=isab_in.454.fa 454_SETTINGS -LR:wqf=no > log.txt
>
>
> and 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 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.
>
> To (un-)subscribe the MIRA mailing lists, see:
> http://www.chevreux.org/mira_mailinglists.html
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>
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>
>
> Compiled by: bach
> Wed Nov 14 23:07:20 CET 2012
> On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC
> 2012 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 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/Linux
>
>
>
> Parsing parameters: --project=isab --job=denovo,genome,accurate,454
> --fasta=isab_in.454.fa 454_SETTINGS -LR:wqf=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), 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] no
>
> 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
> 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.fa
> When 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.fastq
> When 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.txt
> When 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.txt
>
> When 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
>
>
>
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