[mira_talk] MIRA failure
- From: Damien HINSINGER <damien.hinsinger@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 Mar 2015 21:40:58 +0100
Hello,
First, thank you for developing MIRA !
Then, I face to a problem I tried to solve since several days, without success.
I would like to make two round of MIRA 4.9.3 assemblies, the first being on
filtered reads, and the second on merged contigs produced by MIRA, SOAPdenovo
and Oases. The first assembly get well, but the second failed, always at the
same step :
> Aligning possible forward matches:
> [0%] ....|.... [10%] ....|.... [20%] ....|...Failure, wrapped MIRA process
> aborted.
I saw surfing on the net that this problem could be related to memory issues
(both RAM and hard drive memory), but I have 16Go (RAM) and 190Go (hard drive),
so I think this is not an issue. Moreover, I run MIRA with the same manifest
and data on an other computer, and have the same problem, exactly at the same
step.
Here is my manifest :
> # Manifest file for assemblies of library 005
> project = MIRA_assembly_2_lib_005
> job = denovo,est,accurate
> parameters = 'COMMON_SETTINGS -KS:mnr=yes -SK:mmhr=5 SANGER_SETTINGS
> -ALIGN:min_relative_score=95 -ASSEMBLY:minimum_read_length=100 -AS:epoq=no'
>
> readgroup = DataFoIonPairs
> data =
> chip_3-bam_results/library_005/synthaethic_assembly_lib_005_formatted.fa
> technology = sanger
The log :
> This is MIRA 4.9.3_0+g373997a .
>
> 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
>
> After subscribing, mail general questions to the MIRA talk mailing list:
> mira_talk@xxxxxxxxxxxxx
>
>
> To report bugs or ask for features, please use the SourceForge ticketing
> system at:
> http://sourceforge.net/p/mira-assembler/tickets/
> This ensures that requests do not get lost.
>
>
> Compiled by: bach
> Sat Nov 8 19:53:23 CET 2014
> On: Darwin airfau2.fritz.box 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19
> 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
> 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: Darwin MacBook-Pro-de-Damien.local 14.1.0 Darwin Kernel
> Version 14.1.0: Thu Feb 26 19:26:47 PST 2015;
> root:xnu-2782.10.73~1/RELEASE_X86_64 x86_64
>
> Looking for files named in data ...Pushing back filename:
> "chip_3-bam_results/library_005/synthaethic_assembly_lib_005_formatted.fa"
> Manifest:
> projectname: MIRA_assembly_2_lib_005
> job: denovo,est,accurate
> parameters: 'COMMON_SETTINGS -KS:mnr=yes -SK:mmhr=5 SANGER_SETTINGS
> -ALIGN:min_relative_score=95 -ASSEMBLY:minimum_read_length=100 -AS:epoq=no'
> Manifest load entries: 1
> MLE 1:
> RGID: 1
> RGN: DataFoIonPairs SN: StrainX
> SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
> ST: 0 (Sanger) namschem: 1 SID: 0
> DQ: 20
> BB: 0 Rail: 0 CER: 0
>
> chip_3-bam_results/library_005/synthaethic_assembly_lib_005_formatted.fa
> ''
> Parameters parsed without error, perfect.
>
> ------------------------------------------------------------------------------
> Parameter settings seen for:
> Sanger data
>
> Used parameter settings:
> General (-GE):
> Project name : MIRA_assembly_2_lib_005
> 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
> Colour reads by kmer frequency (crkf) : no
> Preprocess only (ppo) : no
>
> Load reads options (-LR):
> Wants quality file (wqf) : [san] yes
>
> Filecheck only (fo) : no
>
> Assembly options (-AS):
> Number of passes (nop) : 0
> Kmer series (kms) :
> Maximum number of RMB break loops (rbl) : 2
> Maximum contigs per pass (mcpp) : 0
>
> Minimum read length (mrl) : [san] 100
> Minimum reads per contig (mrpc) : [san] 2
> Enforce presence of qualities (epoq) : [san] no
>
> Automatic repeat detection (ard) : no
> Coverage threshold (ardct) : [san] 2
> Minimum length (ardml) : [san] 400
> Grace length (ardgl) : [san] 40
> Use uniform read distribution (urd) : no
> Start in pass (urdsip) : 3
> Cutoff multiplier (urdcm) : [san] 1.5
>
> 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) : 720
>
> Strain and backbone options (-SB):
> Bootstrap new backbone (bnb) : [san] yes
> Start backbone usage in pass (sbuip) : 0
> Backbone rail from strain (brfs) :
> Backbone rail length (brl) : 0
> Backbone rail overlap (bro) : 0
> Trim overhanging reads (tor) : yes
>
> (Also build new contigs (abnc)) : yes
>
> Dataprocessing options (-DP):
> Use read extensions (ure) : [san] no
> Read extension window length (rewl) : [san] 30
> Read extension w. maxerrors (rewme) : [san] 2
> First extension in pass (feip) : [san] 0
> Last extension in pass (leip) : [san] 0
>
> Clipping options (-CL):
> SSAHA2 or SMALT clipping:
> Gap size (msvsgs) : [san] 10
> Max front gap (msvsmfg) : [san] 60
> Max end gap (msvsmeg) : [san] 120
> Strict front clip (msvssfc) : [san] 0
> Strict end clip (msvssec) : [san] 0
> Possible vector leftover clip (pvlc) : [san] no
> maximum len allowed (pvcmla) : [san] 18
> Min qual. threshold for entire read (mqtfer): [san] 0
> Number of bases (mqtfernob) : [san] 0
> Quality clip (qc) : [san] yes
> Minimum quality (qcmq) : [san] 20
> Window length (qcwl) : [san] 30
> Bad stretch quality clip (bsqc) : [san] no
> Minimum quality (bsqcmq) : [san] 20
> Window length (bsqcwl) : [san] 30
> Masked bases clip (mbc) : [san] yes
> Gap size (mbcgs) : [san] 20
> Max front gap (mbcmfg) : [san] 40
> Max end gap (mbcmeg) : [san] 60
> Lower case clip front (lccf) : [san] no
> Lower case clip back (lccb) : [san] no
> Clip poly A/T at ends (cpat) : [san] yes
> Keep poly-a signal (cpkps) : [san] yes
> Minimum signal length (cpmsl) : [san] 12
> Max errors allowed (cpmea) : [san] 1
> Max gap from ends (cpmgfe) : [san] 20000
> Clip 3 prime polybase (c3pp) : [san] no
> Minimum signal length (c3ppmsl) : [san] 15
> Max errors allowed (c3ppmea) : [san] 3
> Max gap from ends (c3ppmgfe) : [san] 9
> Clip known adaptors right (ckar) : [san] no
> Ensure minimum left clip (emlc) : [san] no
> Minimum left clip req. (mlcr) : [san] 25
> Set minimum left clip to (smlc) : [san] 30
> Ensure minimum right clip (emrc) : [san] no
> Minimum right clip req. (mrcr) : [san] 10
> Set minimum right clip to (smrc) : [san] 20
>
> Apply SKIM chimera detection clip (ascdc) : no
> Apply SKIM junk detection clip (asjdc) : no
>
> Propose end clips (pec) : [san] no
> Kmer size (peckms) : 25
> Minimum kmer for forward-rev (pmkfr) : 1
> Rare kmer mask (rkm) : [san] no
> Handle Solexa GGCxG problem (pechsgp) : yes
>
> Front freq (pffreq) : [san] 1
> Back freq (pbfreq) : [san] 1
> Front forward-rev (pffore) : [san] no
> Back forward-rev (pbfore) : [san] no
> Front conf. multi-seq type (pfcmst) : [san] no
> Back conf. multi-seq type (pbcmst) : [san] no
> Front seen at low pos (pfsalp) : [san] no
> Back seen at low pos (pbsalp) : [san] no
>
> Clip bad solexa ends (cbse) : [san] no
> Search PhiX174 (spx174) : [san] no
> Filter PhiX174 (fpx174) : [san] no
>
> Parameters for SKIM algorithm (-SK):
> Number of threads (not) : 2
>
> Also compute reverse complements (acrc) : yes
> Kmer size (kms) : 17
> Automatic increase per pass (kmsaipp) : 1
> Kmer size max(kmsmax) : 0
> Kmer save stepping (kss) : 1
> Percent required (pr) : [san] 65
>
> Max hits per read (mhpr) : 30
>
> Filter megahubs (fmh) : yes
> Megahub cap (mhc) : 150000
> Max megahub ratio (mmhr) : 5
>
> SW check on backbones (swcob) : no
>
> Max kmers in memory (mkim) : 15000000
> MemCap: hit reduction (mchr) : 2048
>
> Parameters for Kmer Statistics (-KS):
> Freq. cov. estim. min (fcem) : 30
> Freq. estim. min normal (fenn) : 0.4
> Freq. estim. max normal (fexn) : 1.6
> Freq. estim. repeat (fer) : 1.9
> Freq. estim. heavy repeat (fehr) : 8
> Freq. estim. crazy (fecr) : 20
> Mask nasty repeats (mnr) : yes
> Nasty repeat ratio (nrr) : 100
> Nasty repeat coverage (nrc) : 200
> Lossless digital normalisation (ldn) : yes
>
> Repeat level in info file (rliif) : 6
>
> Million kmers per buffer (mkpb) : 4
> Rare kmer early kill (rkek) : no
>
> Pathfinder options (-PF):
> Use quick rule (uqr) : [san] yes
> Quick rule min len 1 (qrml1) : [san] 200
> Quick rule min sim 1 (qrms1) : [san] 90
> Quick rule min len 2 (qrml2) : [san] 100
> Quick rule min sim 2 (qrms2) : [san] 95
> Backbone quick overlap min len (bqoml) : [san] 150
> Max. start cache fill time (mscft) : 5
>
> Align parameters for Smith-Waterman align (-AL):
> Bandwidth in percent (bip) : [san] 20
> Bandwidth max (bmax) : [san] 130
> Bandwidth min (bmin) : [san] 25
> Minimum score (ms) : [san] 30
> Minimum overlap (mo) : [san] 17
> Minimum relative score in % (mrs) : [san] 95
> Solexa_hack_max_errors (shme) : [san] -1
> Extra gap penalty (egp) : [san] yes
> extra gap penalty level (egpl) : [san] reject_codongaps
> Max. egp in percent (megpp) : [san] 100
>
> Contig parameters (-CO):
> Name prefix (np) :
> MIRA_assembly_2_lib_005
> Reject on drop in relative alignment score in % (rodirs) : [san] 10
> CMinimum relative score in % (cmrs) : [san] -1
> 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
> Minimum neighbour quality needed for tagging (mnq) : [san] 20
> Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
> End-read Marking Exclusion Area in bases (emea) : [san] 25
> Set to 1 on clipping PEC (emeas1clpec) : yes
> Also mark gap bases (amgb) : [san] yes
> Also mark gap bases - even multicolumn (amgbemc) : [san] yes
> Also mark gap bases - need both strands (amgbnbs): [san] yes
> Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
> Merge short reads (msr) : [san] no
> Max errors (msrme) : [san] 0
> Keep ends unmerged (msrkeu) : [san] -1
> Gap override ratio (gor) : [san] 66
>
> Edit options (-ED):
> Mira automatic contig editing (mace) : yes
> Edit kmer singlets (eks) : yes
> Edit homopolymer overcalls (ehpo) : [san] yes
>
> Misc (-MI):
> Large contig size (lcs) : 500
> Large contig size for stats (lcs4s) : 1000
>
> I know what I do (ikwid) : no
>
> Extra flag 1 / sanity track check (ef1) : no
> Extra flag 2 / dnredreadsatpeaks (ef2) : yes
> Extra flag 3 / pelibdisassemble (ef3) : no
> Extended log (el) : no
>
> Nag and Warn (-NW):
> Check NFS (cnfs) : stop
> Check multi pass mapping (cmpm) : stop
> Check template problems (ctp) : stop
> Check SRA read names (csrn) : stop
> Check duplicate read names (cdrn) : stop
> Check max read name length (cmrnl) : stop
> Max read name length (mrnl) : 40
> Check average coverage (cac) : stop
> Average coverage value (acv) : 80
>
> Directories (-DI):
> Top directory for writing files : MIRA_assembly_2_lib_005_assembly
> For writing result files :
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_results
> For writing result info files :
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_info
> For writing tmp files :
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp
> Tmp redirected to (trt) :
> For writing checkpoint files :
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_chkpt
>
> Output files (-OUTPUT/-OUT):
> Save simple singlets in project (sssip) : [san] no
> Save tagged singlets in project (stsip) : [san] 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) : no
> Saved as GFF3 (org3) : no
> Saved as HTML (orh) : no
> Saved as Transposed Contig Summary (ors) : yes
> Saved as simple text format (ort) : yes
> Saved as wiggle (orw) : no
>
> 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 : MIRA_assembly_2_lib_005_out.caf
> MAF : MIRA_assembly_2_lib_005_out.maf
> FASTA : MIRA_assembly_2_lib_005_out.unpadded.fasta
> FASTA quality : MIRA_assembly_2_lib_005_out.unpadded.fasta.qual
> FASTA (padded) : MIRA_assembly_2_lib_005_out.padded.fasta
> FASTA qual.(pad): MIRA_assembly_2_lib_005_out.padded.fasta.qual
> GAP4 (directory): MIRA_assembly_2_lib_005_out.gap4da
> ACE : MIRA_assembly_2_lib_005_out.ace
> HTML : MIRA_assembly_2_lib_005_out.html
> Simple text : MIRA_assembly_2_lib_005_out.txt
> TCS overview : MIRA_assembly_2_lib_005_out.tcs
> Wiggle : MIRA_assembly_2_lib_005_out.wig
> ------------------------------------------------------------------------------
> Deleting old directory MIRA_assembly_2_lib_005_assembly ... done.
> Creating directory MIRA_assembly_2_lib_005_assembly ... done.
> Creating directory
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_results ... done.
> Creating directory
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_info ... done.
> Creating directory
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_chkpt ... done.
> Creating directory
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp ... done.
>
> Tmp directory is not on a NFS mount, good.
>
> Localtime: Thu Mar 12 12:27:32 2015
>
> Loading reads from
> chip_3-bam_results/library_005/synthaethic_assembly_lib_005_formatted.fa type
> fa
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] Checking reads for trace data (loading qualities if
> needed):
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> No SCF data present in any read, EdIt automatic contig editing for Sanger
> data is now switched off.
> 5142 reads with valid data for assembly.
> Localtime: Thu Mar 12 12:27:33 2015
>
> Generated 5142 unique DNA template ids for 5142 valid reads.
> No useful template information found.
> TODO: Like Readpool: strain x has y reads
> Have read pool with 5142 reads.
>
> ===========================================================================
> Backbones: 0 Backbone rails: 0
> Sequencing technology statistics:
>
> Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa Solid
> ------------------------------------------------------------
> Total reads 5142 0 0 0 0 0 0 0
> Reads wo qual 5142 0 0 0 0 0 0 0
> Used reads 5142 0 0 0 0 0 0 0
> Avg. tot rlen 590 0 0 0 0 0 0 0
> Avg. used rlen 590 0 0 0 0 0 0 > 0
> W/o clips 5142 0 0 0 0 0 0 0
>
>
> Readgroup statistics:
> RG 1 Sanger avg total len: 590 avg clip len: 590 total bases:
> 3035685 used bases: 3035685
> ===========================================================================
>
>
> Checking pairs of readgroup 1 (named: 'DataFoIonPairs'): found 0
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_int_clippings_t0.0.txt
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_int_clippings_t1.0.txt
> Post-load clips:
> Localtime: Thu Mar 12 12:27:33 2015
> freemem: 11152535552
> TNH: 5356
> XME 1: 0.000212828
> XME 2: 0.1
> NEPB 1: 104857
> NEPB 2: 104857
> Writing temporary hstat files:
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] done
> Localtime: Thu Mar 12 12:27:33 2015
> Flushing buffers to disk:
> [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%]
> Localtime: Thu Mar 12 12:27:33 2015
> clean up temporary stat files...Localtime: Thu Mar 12 12:27:33 2015
> Localtime: Thu Mar 12 12:27:33 2015
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
>
> ===========================================================================
> Backbones: 0 Backbone rails: 0
> Sequencing technology statistics:
>
> Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa Solid
> ------------------------------------------------------------
> Total reads 5142 0 0 0 0 0 0 0
> Reads wo qual 5142 0 0 0 0 0 0 0
> Used reads 4978 0 0 0 0 0 0 0
> Avg. tot rlen 590 0 0 0 0 0 0 0
> Avg. used rlen 550 0 0 0 0 0 0 > 0
> W/o clips 4428 0 0 0 0 0 0 0
>
>
> Readgroup statistics:
> RG 1 Sanger avg total len: 590 avg clip len: 550 total bases:
> 3035685 used bases: 2737955
> ===========================================================================
>
>
> Sorting reads ... done.
>
> Tmp directory is not on a NFS mount, good.
>
> PRED MAXTID 5141
> No bases clipped in first pec round, skipping second round.
>
> ===========================================================================
> Backbones: 0 Backbone rails: 0
> Sequencing technology statistics:
>
> Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa Solid
> ------------------------------------------------------------
> Total reads 5142 0 0 0 0 0 0 0
> Reads wo qual 5142 0 0 0 0 0 0 0
> Used reads 4978 0 0 0 0 0 0 0
> Avg. tot rlen 590 0 0 0 0 0 0 0
> Avg. used rlen 550 0 0 0 0 0 0 > 0
> W/o clips 4428 0 0 0 0 0 0 0
>
>
> Readgroup statistics:
> RG 1 Sanger avg total len: 590 avg clip len: 550 total bases:
> 3035685 used bases: 2737955
> ===========================================================================
>
>
> Performing snapshot 1
> Localtime: Thu Mar 12 12:27:34 2015
> Creating directory
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_chkpt ... done.
> Localtime: Thu Mar 12 12:27:34 2015
> all-auto determination of passes and kmer series.
> Number of passes used by MIRA: 5
> kmer series: 17, 31, 63, 127, 255
> Could not read file /proc/self/status
> --------------------------------------------------------------------------------
>
>
> Pass: 1 / 5
> Automatic -SK:bph set to 17
>
> ===========================================================================
> Backbones: 0 Backbone rails: 0
> Sequencing technology statistics:
>
> Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa Solid
> ------------------------------------------------------------
> Total reads 5142 0 0 0 0 0 0 0
> Reads wo qual 5142 0 0 0 0 0 0 0
> Used reads 4978 0 0 0 0 0 0 0
> Avg. tot rlen 590 0 0 0 0 0 0 0
> Avg. used rlen 550 0 0 0 0 0 0 > 0
> W/o clips 4428 0 0 0 0 0 0 0
>
>
> Readgroup statistics:
> RG 1 Sanger avg total len: 590 avg clip len: 550 total bases:
> 3035685 used bases: 2737955
> ===========================================================================
>
>
> Localtime: Thu Mar 12 12:27:34 2015
> freemem: 10881335296
> TNH: 2664005
> XME 1: 0.105858
> XME 2: 0.105858
> NEPB 1: 111000
> NEPB 2: 111000
> Writing temporary hstat files:
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] done
> Localtime: Thu Mar 12 12:27:35 2015
> Flushing buffers to disk:
> [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%]
> Localtime: Thu Mar 12 12:27:36 2015
> clean up temporary stat files...Localtime: Thu Mar 12 12:27:36 2015
> Localtime: Thu Mar 12 12:27:36 2015
> Kmer statistics:
> =========================================================
> Using kmers of size: 17
> Measured avg. raw frequency coverage: 11
> Corrected avg. raw frequency coverage: 11
>
> Final average frequency: 11
>
> Deduced thresholds:
> -------------------
> Min normal freq: 4.4
> Max normal freq 17.6
> Repeat freq: 20.9
> Heavy freq: 88
> Crazy freq: 220
> Mask freq: 1100
>
> Repeat ratio histogram:
> -----------------------
> 0 340450
> 1 247780
> 2 46874
> 3 9552
> 4 2630
> 5 578
> 6 184
> 7 114
> 8 50
> 9 12
> 10 4
> 11 28
> 12 12
> 13 4
> 14 6
> 15 2
> 16 2
> 17 2
> 18 2
> 35 2
> 38 2
> 1466 2
> =========================================================
>
> Estimator of average coverage: 28
> Assigning statistics values:
> Localtime: Thu Mar 12 12:27:36 2015
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] Localtime: Thu Mar 12 12:27:38 2015
> Writing read repeat info to:
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_info/MIRA_assembly_2_lib_005_info_readrepeats.lst
> ... 518 sequences with 539 masked stretches.
> Localtime: Thu Mar 12 12:27:38 2015
> Performing digital normalisation:
> Readgroup 1:
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] Calculating replacement coverage
> Digital normalisation: removed 283 reads.
> done
> Localtime: Thu Mar 12 12:27:38 2015
> AS_resumeasembly 0
> AS_resumeisok 0
> fileExists(MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_signal_findpossibleoverlaps_pass.1.ok)
> 0
> Localtime: Thu Mar 12 12:27:38 2015
>
>
> Searching for possible overlaps:
> Localtime: Thu Mar 12 12:27:38 2015
> Now running threaded and partitioned skimmer-17 with 1 partitions in 2
> threads:
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%] done.
>
> truncating
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_int_posmatchf_pass.1.bin
> truncated
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_int_posmatchf_pass.1.bin
> from 657576 to 559776
>
> truncating
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_int_posmatchc_pass.1.bin
> truncated
> MIRA_assembly_2_lib_005_assembly/MIRA_assembly_2_lib_005_d_tmp/MIRA_assembly_2_lib_005_int_posmatchc_pass.1.bin
> from 472632 to 376560
>
>
> Hits chosen: 78028
>
> Localtime: Thu Mar 12 12:27:41 2015
>
> Total megahubs: 2
>
>
> MIRA has detected megahubs in your data.This may not be a problem, but most
> probably is, especially for eukaryotes.
>
> System memory: 1040879616
> Mem2keepfree: 156131942
> Used by MIRA: 0
> Mem avail: 884747674
> rsh not increased.
> Edge vector capacity: 86929
> Can load up to 81929 skim edges at once.
> Partitioning into 1 blocks.
> Blocks: 5142
> We have 78028 skims in file.
> Localtime: Thu Mar 12 12:27:41 2015
> De-normalising SKIM hits ... (this will take a while)
> Localtime: Thu Mar 12 12:27:41 2015
> Localtime: Thu Mar 12 12:27:41 2015
> Writing normalised skimblock 0 ( 2 MiB) ... done.
> Localtime: Thu Mar 12 12:27:41 2015
> Loading block 0
> Only one block, already loaded.
> Localtime: Thu Mar 12 12:27:41 2015
> Step 0
> Loading block 0
> Only one block, already loaded.
> Localtime: Thu Mar 12 12:27:41 2015
> Step 05
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 13599
> Step 10
> Total skims taken: 13599
> Step 20
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 13599
> Step 30
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 14406
> Step 40
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 19426
> Step 50
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 22266
> Step 60
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 22795
> Step 70
> Loading block 0
> Only one block, already loaded.
> Total skims taken: 22829
> Step solexa by critlevel
> rsh4_takeSolexaByCritLevel.
> Loading block 0
> Only one block, already loaded.
> Taken 0 hits.
> rsh4_takeSolexaByCritLevel.
> Loading block 0
> Only one block, already loaded.
> Taken 0 hits.
> Step template overlaps
> Loading block 0
> Only one block, already loaded.
> Step NAO
> rsh4_takeNeedAllOverlaps.
> None needed.
> Total skims taken: 22829
>
> Filtering forward skims.
> Localtime: Thu Mar 12 12:27:41 2015
> Writing reduced skim file:
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Done.
> Done.
> Filtering complement skims.
> Localtime: Thu Mar 12 12:27:41 2015
> Writing reduced skim file:
> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
> [90%] ....|.... [100%]
> Done.
> Done all filtering.
> Localtime: Thu Mar 12 12:27:41 2015
> Making alignments.
> Localtime: Thu Mar 12 12:27:41 2015
>
> Aligning possible forward matches:
> [0%] ....|.... [10%] ....|.... [20%] ....|...Failure, wrapped MIRA process
> aborted.
And my data_file (the first and last 2 sequences) :
> >contig_0
> TCTGATTTTTTTTTTTTTTTTTTTTTTTTTTTTGACGAGCCATGGGATGGCCCGTTGGGAACCCTTTTTTTTTTTTTTTTTTACAGTTAAACATATGGTGGGCCCATCAATAAAACCAAGAAGGCCAATGGCCATCATAGCTCATACTATACCCATGTAGCCAAAGGGCTCTTTTTTGCCTGCATAGTATGCACAATGTGTAAGATTATTCCAAAGCCTGGCAGGATGAGGATATATACTTCTGGGTGACCAAAAAATCAGAACAGGTGTTGATAAAGAATGGGGTCACCACCACCTGAAGGGTCAAAGAAGGTTGTGTTGAGGTTTCGGTCTGTTAGTAGCATTGTAATACCAGCTGCAAGGACCGGCAGAGAGAGAAGTAGTAAGACTGCTGTGATAAGAACAGCTCAAACAAAGAGGGGTGTCTGGTATTGTGAAATTGCAGGGGGTTTTATATTGAGAA
> >contig_1
> TAAACATATGGTGGGCCCATACAATAAAACCAAGAAGGCCAATGGCCATCATAGCTCATACTATACCCATGTAGCCAAAGGGCTCTTTTTTGCCTGCATAGTATGCACAATGTGTAAGATTATTCCAAAGCCTGGCAGGATGAGGATATATACTTCTGGGTGACCAAAAAATCAGAACAGGTGTTGATAAAGAATGGGGTCACCACCACCTGAAGGGTCAAAGAAGGTTGTGTTGAGGTTTCGGTCTGTTAGTAGCATTGTAATACCAGCTGCAAGGACCGGCAGAGAGAGAAGTAGTAAGACTGCTGTGATAAGAACAGCTCAAACAAAGAGGGGTGTCTGGTATTGTGAAATTGCAGGGGGTTTTATATTGAGAATGGTTGTAATAAAGTTAATTGCACCTAAAATTGATGAAATACCTGCTAAGTGAAGGGAGAAAATTGTTTTAGTCTGACAGAAGCTCCGGCATGGGCAAGGTTTCCAGCTAGAGGGGGGTATACTGTTCAGCCTGTACCAGCCCCAGCTTCAACACCAGAAGATGCCAGGAGAAGTAAGAATGATGGAGGAAGGAGCCAAAAACTCATGTTGTTCATGCGAGGAAAGGCCATATCAGGGGCACCGATCATTAGAGGATGAGTCAGTTTCCAAAGCCCCCAATCATGATTGGTATTACTAT
> .....
> >contig_6533
> TTTGAACCATCCTCCCAGCCATCATTCTTATTCTCATCGCCCTCCCTTCACTACGCATCCTCTACCTAATAGACGAAATTAATGACCCACACCTCACAATTAAAGCCATCGGGCACCAATGATACTGAAGCTACGAATACACAGACTATGAAGACCTAGGCTTCGACTCATACATAGTCCCCACACAAGACCTTGCGCCTGGCCAATTCCGACTTCTTGAAGCAGACCATCGAATGGTAGTCCCGATAGAGTCCCCCGTGCGAGTGCTGGTCTCAGCCGAAGACGTGCTGCACTCCTGGGCCGTCCCCTCTCTAGGCGTTAAAATAGACGCAGTTCCTGGTCGACTAAACCAAACAGCATTCATTGCATCCCGGCCAGGGGTTTTCTACGGACAATGCTCAGAGATCTGCGGAGCCAACCACAGCTTTATGCCAATCGTAGTGGAAGCAGTTCCCTTAAACCACTTCGAACACTGATCCTCTTTAATACTTGAAGATGCCTCGCTGAGAAGCTAAACCGGGCCACAGCGTTAGCCTTTTAAGCTAAAGATTGGTGCCTCCCAACCACCCTCAACGACATGCCTCAACTCAACCCCGCACCCTGATTCGCTATCCTAGTATTTTCTTGATTAGTTTTCCTAACAATCCTCCCTGCAAAAGTCTTGGCACACACTTTCCCCAACGAACCAGCCTCGCAAAGCACACAGAAACCTAAAACAGAGCCCTGAAACTGACCATGGCACTAAACTTCTTTGACCAATTTATAAGCCCCACTTACCTAGGAATCCCCCTGATTGCCCTAGCATTAACCCTCCCTTGAATTCTATTTCCAACCCCCTCCTCACGATGACTTAACAACCGCCTTTTAACCCTACAAAGCTGATTCATTAACCGATTTACGTATCAACTACTAATGCCCCTTAACACCGGGGGCCACAAATGAGCCACCATCTTTGCCTCCCTAATACTATTCCTAATTTCCCTAAACATGCTAGGGCTCCTCCCATACACTTTCACACCAACAACCCAACTTTCTATAAACATGGGCTTTGCAGTGCCCCTTTGAATAGCAACAGTCCTAATTGGTATGCGAAACCAACCAACCGCTGCATTAGGCCACCTCCTACCAGAAGGCACCCCCGCCCCTTTAATCCCTGTATTAATTATCATCGAAACAATTAGCTTATTTATTCGCCCCTTGGCCCTAGGCGTTCGACTTACAGCCAATTTAACAGCAGGACATCTTCTGATTCAACTGATCGCAACCGCTGCCTTCGTCCTTCTACCTTTAATGCCAACAGTTGCTATTCTCACCGGGACAGTACTTTTCCTACTAACTATCTTAGAAGTGGCAGTAGCAATAATCCAAGCATACGTCTTCGTCCTACTCCTAAGCCTTTATCTACAAGAAAACGTCTAATGGCCCACCAAGCACACGCATACCACATAGTAGACCCTAGCCCTTGACCGCTGACAGGAGCAGTTGCTGCCCTTTTGATAACCTCCGGCCTCGCCATCTGATTCCACTACCACTCAACAACTTTAATAACAATAGGCCTGGTTCTCTTACTCCTAACAATGTACCAATGATGACGAGACATTGTCCGAGAAGGGACCTTCCAAGGACACCACACTCCTCCTGTCCAGAAAGGCCTTCGATACGGAATGATCCTATTCATCACATCAGAGGTATTCTTCTTTTTAGGGTTCTTCTGAGCCTTCTACCACGCCAGCCTTGCTCCCACCCCAGAACTAGGCGGCTGCTGACCCCCAACAGGCATTACACCCCTTGACCCATTTGAAGTTCCCCTACTCAACACAGCAGTGTTACTTGCATCCGGCGTCACAGTCACATGAGCGCACCACAGCATTATAGAAGGAGAACGTAAACAAGCCATCCACTCCTTAACACTGACGATCCTGCTCGGCTTCTACTTCACCTTCCTTCAAGGCATAGAATATTATGAAGCCCCTTTCACAATTGCCGACGGAGTATATGGCTCCACCTTCTTCGTCGCAACAGGCTTCCATGGCCTTCATGTTATTATTGGCTCTAGCTTCCTGGCTGTCTGCCTCCTACGGCAAGTCCACTACCACTTTACATCCGAACATCACTTTGGATTCGAGGCAGCAGCTTGATACTGACACTTCGTAGACGTAGTATGACTCTTCCTCTACATCTCTATTTATTGATGAGGCTCATAATCTTTCTAGTATTAAAGTTAGTACAAGTGACTTCCAATCACCTAGTTTTGGTTAAAGCCCAAAGAAAGATAATGAATTTAATCACCACCGTAATCACCATCGCTGTCATTTTATCCTCCATTCTAGCAATCGTCTCCTTCTGACTACCAATAATGAGCCCAGACCAAGAAAAACTCTCCCCCTACGAATGTGGTTTCGACCCCCTAGGATCGGCACGCTTACCTTTCTCCCTACGATTCTTCCTAGTGGCGATTCTGTTCCTGCTCTTTGACCTAGAAATTGCCCTCCTTCTCCCCTTACCTTGAGGGGACCAACTTCCCTCC
> >contig_6534
> TTTTGGCTCCTTCCTCCATCATTCTTACTTCTCCTGGCATCTTCTGGTGTTGAAGCTGGGGCTGGTACAGGCTGAACAGTATACCCCCCTCTAGCTGGAAACCTTGCCCATGCCGGAGCTTCTGTCGACCTAACAATTTTCTCCCTTCACTTAGCAGGTATTTCATCAATTTTAGGTGCAATTAACTTTATTACAACCATTCTCAATATAAAACCCCCTGCAATTTCACAATACCAGACACCCCTCTTTGTTTGAGCTGTTCTTATCACAGCAGTCTTACTACTTCTCTCTCTGCCGGTCCTTGCAGCTGGTATTACAATGCTACTAACAGACCGAAACCTCAACACAACCTTCTTTGACCCTTCAGGTGGTGGTGACCCCATTCTTTATCAACACCTGTTCTGATTTTTTGGTCACCCAGAAGTATATATCCTTATCCTGCCAGGCTTTGGAATAATCTCACACATTGTTGCATACTATGCAGGCAAAAAAGAGCCCTTTGGCTACATGGGTATAGTATGAGCTATGATGGCCATTGGCCTTCTTGGTTTTATTGTATGGGCCCACCATATGTTTACTGTTGGTATAGATGTAGATACACGAGCATACTTTACATCAGCAACAATAATTATTGCCATCCCAACGGGTGTTAAAGTCTTTAGCTGACTTGCCACCCTTCATGGAGGGGCAATCAAATGAGAGACCCCTCTTCTATGATCCCTTGGGTTTATTTTCCTTTTCACAGTAGGAGGCCTAACAGGCATTGTTCTAGCTAATTCATCCCTTGATATTACACTACATGACACCTATTATGTAGTAGCCCACTTCCACTATGTCCTCTCTATAGGAGCAGTATTTGCCATCATAGCTGGTTTTGTTCACTGATTCCCCTTACTCACTGGCTTCACCCTACACAGCACATGATCAAAAATTCACTTTGGCGTAATATTTGTAGGCGTTAACCTAACCTTCTTCCCACAACACTTCCTTGGATTAGCAGGCATGCCACGGCGATACTCAGACTACCCAGATGCCTACACTCTTTGAAACACAGTTTCATCCCTGGGATCCCTAATCTCTCTCACTGCTGTTATTATATTCTTATTTATTATCTGAGAAGCATTTGCTGCTAAACGTGTGGTGTCAGGAGTAGAACTCACTGCCACAAATATTGAGTGATTGCATGGCTGCCCTCCACCTTATCACACATTTGAAGAGCCTGCATTCGTTCAAGTTCAACAAGCCCACTAACGAGAAAGGGAGGACTCGAACCCCCATAAACTGGTTTCAAGCCAGCCACAAAACCCTTCTGTCACTTTCTTAATAAGATACTAGTATAGCTGACAATACACTGCTTTGTCAAGGCAGAATCGCGGGTTAAATCCCCGCGTGTCTTATTTAATGGCCCACCCCTCACAATTAGGTTTCCAAGATGCAGCATCCCCAGTCATAGAAGAGCTTCTTCACTTTCATGATCATGCCCTAATAATTGTTTTTCTCATTAGCACTCTTGTCCTTTACATTATTGTGGCAATAGTCTCCACTCGCCTCACGAATATGTATATCCTAGACTCCCAAGAAATTGAAATCATCTGAACCATCCTTCCTGCCATCATCCTCATCCTTATTGCCCTCCCCTCTTTACGAATTCTCTACCTTATGGACGAAATTAATAACCCCCACCTTACAGTTAAGGCAATCGGACACCAATGATACTGAAGCTACGAGTATACTGACTACCAAGAAATTGCCTTTGACTCTTATATGGTCCCAACACAAGACCTGGCCCCTGGACAATTCCGCCTATTAGAAGTGGACCACCGAATAGTTGTGCCCACTGAAGCCCCCATTCGGGTCCTAGTGACAGCAGAAGATGTCTTACACTCATGAGCAGTTCCTGCTCTTGGCGTGAAAATAGATGCAGTTCCAGGACGCCTCAATCAAACAGCCTTCATTGCCTCCCGCCCTGGGGTTTTCTATGGTCAGTGCTCAGAAATCTGTGGTGCAAACCACAGCTTCATGCCCATTGTAGTAGAAGCAGTCCCTCTAAAATACTTCCAAGATTGATCCACACTAATGCTTGAAGACGCCTCACTAAGAAGCTAAACAGGGCCACAGCGTCAGCCTTTTAAGCTGAAGATTGGTGCCTCCCAAACACCCTTAGTGACATGCCTCAATTAAACCCCGCCCCTTGGTTTGCCATTTTAGTCTTTTCTTGACTTGTTTTTGTTACAATTGTAGTACCAAAAGTTCTCAATTATACTTTCCCCAATGAACCAACACCCCAAAGCACTCAAATTCCCAAAACAGACCCTTGAACCTGACCATGATAACAAGCTTCTTTGACCAGTTTATAAGCCCCACCTACCTGGGCATCCCCCTAATAGCCCTTGCTTTTGTCCTCCCTTGACTCCTCTTCCCCTCCCCTGCCCCCCGATGAATTAACAACCGATTCCTTACACTCCAGGGGTGATTCATTAATCGCTTTACATCACAACTCCTCTCCCCTATAAATGTAGGAGGGCACACCTGAGCCCTCATCCTGGCCTCATTAATAACATTCCTACTTTCCCTAAACATACTAGGCCTTCTTCCCTACACTTTCACCCCTACTACCCAACTATCTTTAAACATGGGACTTGCTGTACCCCTATGACTTGCCACTGTAATTATCGGCCTCCGAAATCAACCAACAGCTGCCCTTGGGCACCTACTACCAGAGGGCACCCCAGTCCCCCTCATCCCTGTACTAATCATTATCGAAACAATTAGCCTCTTTATTCGACCCCTCGCCCTCGGAGTCCGACTAACAGCAAACCTAACAGCAGGCCACCTACTAATGCAACTAATTGCAACTGCAGCCTTTGTGTTAGTACCAATAATGCCCACAGTGGCACTTCTCACTTCTATTGTACTCCTACTTCTAACAATCCTAGAGGTTGCAGTTGCTATAATTCAAGCATATGTTTTTGTTCTCCTCTTAAGCCTCTACCTACAAGAAAATGTTTAATGGCCCACCAAGCACATGCATACCACATAGTAGACCCTAGCCCATGACCCCTTACAGGAGCAGTTGCTGCTCTCCTAATAACCTCCGGCCTTGCCATTTGATTCCACTACAACAAAATGTCACTAATAGTATTAGGAACTATCCTTCTTCTACTTACAATGTATCAGTGATGACGAGATATTGTACGAGAAGGCACATATCAAGGACATCACACCCCTCCTGTCCAAAAAGGTCTCCGATATGGGATGATCCTCTTCATCACATCAGAAGTATTCTTTTTCCTTGGCTTTTTCTGAGCCTTTTTCCACTCCAGCCTTGCCCCTACACCTGAAATTGGAGGATGCTGACCCCCAACAGGCATTACCCCTCTGGACCCCTTTGGTGTGCCCCTGCTGAACACAGCAGTACTTCTAGCCTCGGGGGTGACAGTAACATGAGCCCACCACAGCATTATAGAAGGTGAACGAAAACAAACCATTCAAGCACTTGCCTTGACAATTCTATTAGGATGCTACTTCACCTTCCTACAAGGAATGGAGTACTATGAAGCCCCCTTCACAATTGCAGATGGTGTCTATGGCTCAACATTCTTTGTAGCCACAGGATTCCATGGCCTCCATGTCATCATTGGAACCTCATTCCTTGCTGTCTGCCTTCTTCGACAAGTTAACTACCACTTTACAATAGAGCACCACTTTGGGTTTGAAGCAGCAGCTTGATACTGACACTTTGTTGATGTAGTTTGACTATTCCTTTATATCTCTATCTACTGATGAGGATCCTATCTTTCTAGTACTAATGCTAGTATTAGTGACTTCCAATCACCAGGTCTTGGTTAAACCCCAAGGAAAGATAATGAACCTTATTATAACAGTAATTTTT
Any help ?
Thanks in advance, Damien
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
