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Old 07-21-2011, 05:44 AM   #1
jmpi
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Location: germany

Join Date: Jul 2011
Posts: 3
Default Mira assembly

Hi,

I tried my first assembly with mira and used standard parameters (--job=denovo,genome,normal,454).

I wonder why my assembly is so short because my longest contig reached only 17 kb.

Are there possibilities to change thresholds for mira or to improve the length of contigs?

Thanks for your help.
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Old 07-21-2011, 06:04 AM   #2
Eric Fournier
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Do you have the genome of a closely related organism that you could use as a backbone? If so, search for "backbone" in the MIRA3 reference.
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Old 05-21-2013, 04:18 AM   #3
pari_89
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Quote:
Originally Posted by Eric Fournier View Post
Do you have the genome of a closely related organism that you could use as a backbone? If so, search for "backbone" in the MIRA3 reference.
Hi, I want to use a backbone to do a reference-guided assembly using MIRA3. Can anyone please give me the exact command lines and step by step process to run the assembly.

I am using iontorrent data and I have a fastq file format.
My backbone is in fasta format.

Thank you.
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Old 05-21-2013, 04:28 AM   #4
JackieBadger
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Location: Halifax, Nova Scotia

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Quote:
Originally Posted by pari_89 View Post
Hi, I want to use a backbone to do a reference-guided assembly using MIRA3. Can anyone please give me the exact command lines and step by step process to run the assembly.

I am using iontorrent data and I have a fastq file format.
My backbone is in fasta format.

Thank you.
The MIRA documentation is very good and thorough. Just read the manual.
Also, use the MIRA help mailing list.
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Old 05-21-2013, 04:30 AM   #5
GenoMax
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Quote:
Originally Posted by pari_89 View Post
Can anyone please give me the exact command lines and step by step process to run the assembly.

I am using iontorrent data and I have a fastq file format.
My backbone is in fasta format.

Thank you.
Even if we were able do that you may want to read the documentation for MIRA3 and decide for yourself what switches you want to use.

For Ion Torrent data MIRA developers are recommending that one use the development version (v.3.9.10) that you will probably want to install. Here is the section on assembly using Ion Torrent data for the development version.
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Old 06-25-2013, 07:54 AM   #6
pari_89
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Thanks for the link. I will try the new version as well but since I am doing some research on the previous version I was wondering if anyone has the exact command lines.

I just want to map one fastq file to a reference file in fasta format and make it work and then I can go deeper with the switches.

If anyone has managed to do that with iontorrent data, can you please help me?

Thank you.

Kind Regards

Parinita.
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Old 06-25-2013, 01:59 PM   #7
pag
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using version 3.9, the following "worked" on 454 data

This was a situation where I had already largely determined the sequence using a denovo assembly, using information also from newbler and phred/phrap/consed

But here's my mira manifest file.
Code:
project = remap09
job = genome,mapping,accurate
parameters = COMMON_SETTINGS -SK:mmhr=2,swcob=yes -HS:mnr=no -MI:lcs=700 -NW:somrnl=0 -GE:not=3,kpmf=10 -AS:urd=no -OUT:ora=yes -SB:sbuip=1 -CL:ascdc=no,pechsgp=no \
  454_SETTINGS -CL:pec=yes,pvlc=no,pvcmla=50,mbc=no,lccf=yes,lccb=yes -DP:ure=no -AL:egp=no -ED:ace=yes

readgroup = data454
data = 454full.fastq
technology = 454

readgroup = mapgrp
data = refmap.fastq
technology = text
as_reference
some reads appeared to be in error, resulting in some other reads NOT mapping to the reference, so make sure to re-map/re-assemble your debris.
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Old 07-17-2013, 11:52 PM   #8
pari_89
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hi everyone, I am currently using mira for a mapping assembly. My manifest file is like this :
project = bsb_assembly
job = genome,mapping,accurate
parameters = -GE:not=8

# The second part defines the sequencing data MIRA should load and assemble
# The data is logically divided into "readgroups": this reflects the
# ... that read sequences ...


readgroup = bsb1_in
data = bsb1_in.iontor.fastq
technology = iontor

readgroup = bsb
data = bsb1_backbone_in.fna


However, I have the impression that the bsb1_backbone_in.fna is treated like a file containing reads. I want to map the reads in bsb1_in.iontor.fastq to an already annotated gbk or fasta file. I have done this in mira by just naming the fasta file as backbone but in the manifest file, I just want to specify my .fna file is a complete genome in itself.

Can anyone please help with this?

Thank you.
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Old 07-18-2013, 02:09 AM   #9
mastal
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Default Mira assembly

Have you seen this discussionon on the Mira mailing lists?

http://www.freelists.org/post/mira_t...ference-genome

It might help with your problem.
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Old 07-24-2014, 03:25 AM   #10
madhubioinfo
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hello all,
i have bacterial genome of around R1=6194592,R2=6194592 paired reads around 2.5 Gb illumina data i would like to perform mira assembly for my data i cannot abtle run , its giving memory error but i have 48 GB RAM SGE cluster am including my manifest file and my assembly log also , please find it and help me in running mira

project = Lyngbya_assembly
job = genome,denovo,accurate

readgroup = MyPairedEnd151bpLib
data = /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R1.fastq /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R2.fastq
technology = solexa
strain= Lyngyba_assembly
template_size = 130 480


parameters = COMMON_SETTINGS -NW:somrnl=100 -GE:not=4 -AS:urd=no -HS:mnr

Your system seems to be older or have some quirks with locale settings.
Using the LC_ALL=C workaround.
If you don't want that, fix your system ;-)
This is MIRA 3.9.18 ().

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@freelists.org

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
Mon Jul 1 21:16:33 CEST 2013
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 iicb.sequencer.cluster 2.6.18-238.19.1.el5 #1 SMP Fri Jul 15 07:31:24 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux

Looking for files named in data ...Pushing back filename: "/data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R1.fastq"
Pushing back filename: "/data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R2.fastq"
Manifest:
projectname: Lyngbya_assembly
job: genome,denovo,accurate
parameters: COMMON_SETTINGS -NW:somrnl=100 -GE:not=4 -AS:urd=no -HS:mnr
Manifest load entries: 1
MLE 1:
RGID: 1
RGN: MyPairedEnd151bpLib SN: Lyngyba_assembly
SP: SPio: 0 SPC: 0 IF: 130 IT: 480 TSio: 0
ST: 6 (Solexa) namschem: 4 SID: 0
DQ: 30
BB: 0 Rail: 0 CER: 0

/data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R1.fastq /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R2.fastq

Parameters parsed without error, perfect.

-CLec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data

Used parameter settings:
General (-GE):
Project name : Lyngbya_assembly
Number of threads (not) : 4
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 hash frequency (crhf) : yes

Load reads options (-LR):
Wants quality file (wqf) : [sxa] yes

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
Maximum contigs per pass (mcpp) : 0

Minimum read length (mrl) : [sxa] 20
Minimum reads per contig (mrpc) : [sxa] 10
Enforce presence of qualities (epoq) : [sxa] yes

Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [sxa] 2.5
Minimum length (ardml) : [sxa] 300
Grace length (ardgl) : [sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [sxa] 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):
Start backbone usage in pass (sbuip) : 3
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) : [sxa] no
Read extension window length (rewl) : [sxa] 30
Read extension w. maxerrors (rewme) : [sxa] 2
First extension in pass (feip) : [sxa] 0
Last extension in pass (leip) : [sxa] 0

Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [sxa] 1
Max front gap (msvsmfg) : [sxa] 2
Max end gap (msvsmeg) : [sxa] 2
Strict front clip (msvssfc) : [sxa] 0
Strict end clip (msvssec) : [sxa] 0
Possible vector leftover clip (pvlc) : [sxa] no
maximum len allowed (pvcmla) : [sxa] 18
Min qual. threshold for entire read (mqtfer): [sxa] 5
Number of bases (mqtfernob) : [sxa] 15
Quality clip (qc) : [sxa] no
Minimum quality (qcmq) : [sxa] 20
Window length (qcwl) : [sxa] 30
Bad stretch quality clip (bsqc) : [sxa] no
Minimum quality (bsqcmq) : [sxa] 5
Window length (bsqcwl) : [sxa] 20
Masked bases clip (mbc) : [sxa] no
Gap size (mbcgs) : [sxa] 5
Max front gap (mbcmfg) : [sxa] 12
Max end gap (mbcmeg) : [sxa] 12
Lower case clip front (lccf) : [sxa] no
Lower case clip back (lccb) : [sxa] no
Clip poly A/T at ends (cpat) : [sxa] no
Keep poly-a signal (cpkps) : [sxa] no
Minimum signal length (cpmsl) : [sxa] 12
Max errors allowed (cpmea) : [sxa] 1
Max gap from ends (cpmgfe) : [sxa] 9
Clip 3 prime polybase (c3pp) : [sxa] yes
Minimum signal length (c3ppmsl) : [sxa] 12
Max errors allowed (c3ppmea) : [sxa] 2
Max gap from ends (c3ppmgfe) : [sxa] 9
Clip known adaptors right (ckar) : [sxa] yes
Ensure minimum left clip (emlc) : [sxa] no
Minimum left clip req. (mlcr) : [sxa] 0
Set minimum left clip to (smlc) : [sxa] 0
Ensure minimum right clip (emrc) : [sxa] no
Minimum right clip req. (mrcr) : [sxa] 10
Set minimum right clip to (smrc) : [sxa] 20

Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no

Propose end clips (pec) : [sxa] yes
Bases per hash (pecbph) : 31
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [sxa] 0
Back freq (pbfreq) : [sxa] 0
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [sxa] yes
Back forward-rev (pbfore) : [sxa] yes
Front conf. multi-seq type (pfcmst) : [sxa] yes
Back conf. multi-seq type (pbcmst) : [sxa] yes
Front seen at low pos (pfsalp) : [sxa] no
Back seen at low pos (pbsalp) : [sxa] no

Clip bad solexa ends (cbse) : [sxa] yes
Search PhiX174 (spx174) : [sxa] yes
Filter PhiX174 (fpx174) : [sxa] no

Rare kmer mask (rkm) : [sxa] 0

Parameters for SKIM algorithm (-SK):
Number of threads (not) : 4

Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 23
Hash save stepping (hss) : 1
Percent required (pr) : [sxa] 95

Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 0

SW check on backbones (swcob) : no

Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 4096

Parameters for Hash Statistics (-HS):
Freq. cov. estim. min (fcem) : 0
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) : no
Nasty repeat ratio (nrr) : 100
Nasty repeat coverage (nrc) : 0
Lossless digital normalisation (ldn) : no

Repeat level in info file (rliif) : 6

Pathfinder options (-PF):
Use quick rule (uqr) : [sxa] yes
Quick rule min len 1 (qrml1) : [sxa] -95
Quick rule min sim 1 (qrms1) : [sxa] 100
Quick rule min len 2 (qrml2) : [sxa] -85
Quick rule min sim 2 (qrms2) : [sxa] 100
Backbone quick overlap min len (bqoml) : [sxa] 20
Max. start cache fill time (mscft) : 5

Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [sxa] 20
Bandwidth max (bmax) : [sxa] 80
Bandwidth min (bmin) : [sxa] 20
Minimum score (ms) : [sxa] 15
Minimum overlap (mo) : [sxa] 25
Minimum relative score in % (mrs) : [sxa] 90
Solexa_hack_max_errors (shme) : [sxa] -1
Extra gap penalty (egp) : [sxa] no
extra gap penalty level (egpl) : [sxa] low
Max. egp in percent (megpp) : [sxa] 100

Contig parameters (-CO):
Name prefix (np) : Lyngbya_assembly
Reject on drop in relative alignment score in % (rodirs) : [sxa] 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) : [sxa] 4
Minimum neighbour quality needed for tagging (mnq) : [sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [sxa] 30
End-read Marking Exclusion Area in bases (emea) : [sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [sxa] yes
Also mark gap bases - need both strands (amgbnbs): [sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [sxa] no
Merge short reads (msr) : [sxa] yes
Max errors (msrme) : [sxa] 0
Keep ends unmerged (msrkeu) : [sxa] -1
Gap override ratio (gor) : [sxa] 66

Edit options (-ED):
Automatic contig editing (ace) : [sxa] no
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50

Misc (-MI):
Extended log (el) : no
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 5000
Extra flag 1 / sanity track check (ef1) : no
Extra flag 2 / dnredreadsatpeaks (ef2) : yes

Nag and Warn (-NW):
Stop on max read name length (somrnl) : 100
Stop on NFS (sonfs) : yes
Stop on template problems (sote) : yes
Stop on duplicate read names (sodrn) : yes

Directories (-DI):
Working directory :
Top directory for writing files : Lyngbya_assembly_assembly
For writing result files : Lyngbya_assembly_assembly/Lyngbya_assembly_d_results
For writing result info files : Lyngbya_assembly_assembly/Lyngbya_assembly_d_info
For writing tmp files : Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : Lyngbya_assembly_assembly/Lyngbya_assembly_d_chkpt

Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [sxa] no
Save tagged singlets in project (stsip) : [sxa] 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) : 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 : Lyngbya_assembly_out.caf
MAF : Lyngbya_assembly_out.maf
FASTA : Lyngbya_assembly_out.unpadded.fasta
FASTA quality : Lyngbya_assembly_out.unpadded.fasta.qual
FASTA (padded) : Lyngbya_assembly_out.padded.fasta
FASTA qual.(pad): Lyngbya_assembly_out.padded.fasta.qual
GAP4 (directory): Lyngbya_assembly_out.gap4da
ACE : Lyngbya_assembly_out.ace
HTML : Lyngbya_assembly_out.html
Simple text : Lyngbya_assembly_out.txt
TCS overview : Lyngbya_assembly_out.tcs
Wiggle : Lyngbya_assembly_out.wig
------------------------------------------------------------------------------
Deleting old directory Lyngbya_assembly_assembly ... done.
Creating directory Lyngbya_assembly_assembly ... done.
Creating directory Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp ... done.
Creating directory Lyngbya_assembly_assembly/Lyngbya_assembly_d_results ... done.
Creating directory Lyngbya_assembly_assembly/Lyngbya_assembly_d_info ... done.
Creating directory Lyngbya_assembly_assembly/Lyngbya_assembly_d_chkpt ... done.

Tmp directory is not on a NFS mount, good.

Localtime: Wed Jul 23 20:25:53 2014

Loading reads from /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R1.fastq type fastq
Localtime: Wed Jul 23 20:25:53 2014
Loading data from FASTQ file: /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R1.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)


Done.
Loaded 6194592 reads, Localtime: Wed Jul 23 20:26:16 2014
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Loading reads from /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R2.fastq type fastq
Localtime: Wed Jul 23 20:26:16 2014
Loading data from FASTQ file: /data/results/STLab/BGAGenomes/Genotypic/WGS/June2014/SO_2511_WGS/Lyngbya/SO_2511_01_R2.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)


Done.
Loaded 6194592 reads, Localtime: Wed Jul 23 20:26:45 2014
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
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, automatic contig editing for Sanger data is now switched off.
12389184 reads with valid data for assembly.
Localtime: Wed Jul 23 20:27:05 2014

Generated 6194592 unique DNA template ids for 12389184 valid reads.
TODO: Like Readpool: strain x has y reads
Have read pool with 12389184 reads.

===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 12389184 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 12389184 0
Avg tot rlen 0 0 0 0 0 0 101 0
Avg rlen used 0 0 0 0 0 0 101 0
W/o clips 0 0 0 0 0 0 12389184 0

Solexa total bases: 1251307584 used bases in used reads: 1251307584
===========================================================================


Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_clippings_t0.0.txt
Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_clippings_t1.0.txt
Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_clippings_t2.0.txt
Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_clippings_t3.0.txt
Post-load clips:
Localtime: Wed Jul 23 20:27:18 2014
Writing temporary hstat files:
freemem: 3763204096
TNH: 5356
XME 1: 0.000212828
XME 2: 0.1
NEPB 1: 104857
NEPB 2: 104857
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Localtime: Wed Jul 23 20:27:18 2014

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Localtime: Wed Jul 23 20:27:18 2014
clean up temporary stat files...Localtime: Wed Jul 23 20:27:18 2014
Raw MHI: 5356
Raw avg. freq. : 1
HSS 10712 HSST: 9641
Localtime: Wed Jul 23 20:27:19 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
CLIP MSG: Adaptor right found: 13573

===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 12389184 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 12212029 0
Avg tot rlen 0 0 0 0 0 0 101 0
Avg rlen used 0 0 0 0 0 0 100 0
W/o clips 0 0 0 0 0 0 12100705 0

Solexa total bases: 1251307584 used bases in used reads: 1230091545
===========================================================================


Sorting reads ... done.

Tmp directory is not on a NFS mount, good.

Hash analysis for proposed cutbacks:Localtime: Wed Jul 23 20:29:15 2014
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Localtime: Wed Jul 23 20:36:53 2014

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Localtime: Wed Jul 23 20:48:35 2014
clean up temporary stat files...Localtime: Wed Jul 23 20:48:39 2014
Raw MHI: 107325367
Raw avg. freq. : 23
HSS 124081212 HSST: 111673091
Localtime: Wed Jul 23 20:49:22 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 23
Corrected avg. raw frequency coverage: 23

Final average frequency: 23

Deduced thresholds:
-------------------
Min normal cov: 9.2
Max normal cov: 36.8
Repeat cov: 43.7
Heavy cov: 184
Crazy cov: 460
Mask cov: 2300

Repeat ratio histogram:
-----------------------
0 100384124
1 11313264
2 3779244
3 6879888
4 1475190
5 167688
6 30710
7 8152
8 5432
9 5032
10 2372
11 1870
12 3394
13 3566
14 2840
15 1868
16 1376
17 1428
18 1248
19 1340
20 1134
21 824
22 870
23 664
24 510
25 670
26 496
27 380
28 552
29 284
30 222
31 136
32 150
33 94
34 70
35 166
36 106
37 104
38 150
39 184
40 298
41 214
42 238
43 204
44 220
45 240
46 300
47 342
48 398
49 260
50 206
51 104
52 72
53 22
55 4
58 2
59 2
62 2
73 2
75 4
79 8
87 8
88 14
89 4
95 12
96 10
108 20
109 6
110 12
111 6
112 4
113 4
114 8
115 4
116 4
117 8
118 16
119 36
120 14
121 16
122 2
124 4
125 4
126 2
129 18
130 4
131 4
133 6
138 6
141 6
142 10
143 4
270 2
=========================================================

Assigning statistics values:
Localtime: Wed Jul 23 20:49:24 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Localtime: Wed Jul 23 20:50:47 2014
Localtime: Wed Jul 23 20:50:47 2014

Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 2185335
Num reads cliped right: 2402388
Num reads completely killed: 638052
Total bases clipped : 154095906

Clipping dubious poly-base stretches at end of reads ... Hash analysis for proposed cutbacks:Localtime: Wed Jul 23 20:51:13 2014
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Localtime: Wed Jul 23 20:55:32 2014

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Localtime: Wed Jul 23 21:00:20 2014
clean up temporary stat files...Localtime: Wed Jul 23 21:00:23 2014
Raw MHI: 85401561
Raw avg. freq. : 26
HSS 100435998 HSST: 90392399
Localtime: Wed Jul 23 21:00:58 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 26
Corrected avg. raw frequency coverage: 26

Final average frequency: 26

Deduced thresholds:
-------------------
Min normal cov: 10.4
Max normal cov: 41.6
Repeat cov: 49.4
Heavy cov: 208
Crazy cov: 520
Mask cov: 2600

Repeat ratio histogram:
-----------------------
0 78240102
1 10337462
2 5783444
3 5392626
4 564662
5 62264
6 12048
7 6152
8 5500
9 2442
10 2424
11 4360
12 3378
13 2436
14 1654
15 1566
16 1392
17 1528
18 1132
19 914
20 928
21 522
22 768
23 546
24 454
25 562
26 296
27 180
28 138
29 154
30 76
31 178
32 112
33 124
34 198
35 290
36 246
37 280
38 240
39 262
40 260
41 378
42 398
43 372
44 258
45 136
46 72
47 22
48 2
49 2
51 4
52 2
55 2
65 2
66 2
67 2
78 2
104 2
105 4
106 2
115 6
116 2
122 6
125 8
126 12
=========================================================

Assigning statistics values:
Localtime: Wed Jul 23 21:00:59 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Localtime: Wed Jul 23 21:02:08 2014
Localtime: Wed Jul 23 21:02:08 2014

Looking for proposed cutbacks ... done.
Performed clips:
Num reads cliped left: 740473
Num reads cliped right: 39143
Num reads completely killed: 31807
Total bases clipped : 1784892

Clipping dubious poly-base stretches at end of reads ...
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 12389184 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 11542477 0
Avg tot rlen 0 0 0 0 0 0 101 0
Avg rlen used 0 0 0 0 0 0 93 0
W/o clips 0 0 0 0 0 0 8188788 0

Solexa total bases: 1251307584 used bases in used reads: 1073962601
===========================================================================


Performing snapshot 1
Localtime: Wed Jul 23 21:02:25 2014
Creating directory Lyngbya_assembly_assembly/Lyngbya_assembly_d_chkpt ... done.
Localtime: Wed Jul 23 21:04:03 2014
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 1%
Tgid: 1389
Pid: 1389
PPid: 27991
TracerPid: 0
Uid: 506 506 506 506
Gid: 507 507 507 507
FDSize: 256
Groups: 100 507
VmPeak: 16095472 kB
VmSize: 16085228 kB
VmLck: 0 kB
VmHWM: 15777456 kB
VmRSS: 15776836 kB
VmData: 16024460 kB
VmStk: 92 kB
VmExe: 5524 kB
VmLib: 0 kB
VmPTE: 30892 kB
StaBrk: 05c62000 kB
Brk: 3d5eda000 kB
StaStk: 7fff0bf4c580 kB
Threads: 1
SigQ: 0/399360
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,ffffffff
Mems_allowed: 00000000,00000003
--------------------------------------------------------------------------------


Pass: 1 / 4

===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0

Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 12389184 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 11542477 0
Avg tot rlen 0 0 0 0 0 0 101 0
Avg rlen used 0 0 0 0 0 0 93 0
W/o clips 0 0 0 0 0 0 8188788 0

Solexa total bases: 1251307584 used bases in used reads: 1073962601
===========================================================================


Localtime: Wed Jul 23 21:04:05 2014
Writing temporary hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Flushing buffers to disk:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done
Localtime: Wed Jul 23 21:09:01 2014

Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Localtime: Wed Jul 23 21:14:51 2014
clean up temporary stat files...Localtime: Wed Jul 23 21:14:53 2014
Raw MHI: 89468313
Raw avg. freq. : 29
HSS 105062606 HSST: 94556346
Localtime: Wed Jul 23 21:15:29 2014
Hash statistics:
=========================================================
Measured avg. raw frequency coverage: 29
Corrected avg. raw frequency coverage: 29

Final average frequency: 29

Deduced thresholds:
-------------------
Min normal cov: 11.6
Max normal cov: 46.4
Repeat cov: 55.1
Heavy cov: 232
Crazy cov: 580
Mask cov: 2900

Repeat ratio histogram:
-----------------------
0 83234768
1 9932086
2 5646412
3 5550576
4 570654
5 66956
6 13976
7 7024
8 6344
9 2608
10 2510
11 4462
12 3778
13 2798
14 1772
15 1558
16 1452
17 1478
18 1200
19 892
20 1038
21 616
22 648
23 654
24 524
25 582
26 350
27 264
28 178
29 170
30 72
31 106
32 164
33 158
34 130
35 232
36 306
37 276
38 214
39 232
40 330
41 250
42 352
43 610
44 304
45 202
46 114
47 34
48 6
49 2
50 6
51 6
52 8
54 12
57 2
58 6
59 2
60 2
61 2
62 4
70 4
71 4
72 2
73 6
74 2
77 2
78 4
80 4
82 2
83 2
88 4
94 2
95 4
96 4
99 4
107 2
108 6
110 4
112 2
114 8
115 20
116 12
117 2
119 2
173 2
175 8
182 2
399 2
427 2
428 2
429 2
431 4
434 2
=========================================================

Assigning statistics values:
Localtime: Wed Jul 23 21:15:31 2014
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Localtime: Wed Jul 23 21:16:48 2014
Buntifying reads (this may take a while) ... done.
Writing read repeat info to: Lyngbya_assembly_assembly/Lyngbya_assembly_d_info/Lyngbya_assembly_info_readrepeats.lst ... 104931 sequences with 121107 masked stretches.
AS_resumeasembly 0
AS_resumeisok 0
fileExists(Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_signal_findpossibleoverlaps_pass.1.ok) 0
Localtime: Wed Jul 23 21:17:15 2014


Searching for possible overlaps:
Localtime: Wed Jul 23 21:17:15 2014
Now running threaded and partitioned skimmer with 72 partitions in 4 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] done.

truncating Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_posmatchf_pass.1.bin
truncated Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_posmatchf_pass.1.bin from 6846123792 to 3810756072

truncating Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_posmatchc_pass.1.bin
truncated Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_posmatchc_pass.1.bin from 6608385024 to 3759936288


Hits chosen: 630891030

Localtime: Wed Jul 23 22:27:16 2014

Total megahubs: 0
Cutting back possible chimeras ... done.
Chimeras were searched for ... looking for hits to purge.
truncating Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_posmatchf_pass.1.bin from 3810756072 to 3807957744
truncating Lyngbya_assembly_assembly/Lyngbya_assembly_d_tmp/Lyngbya_assembly_int_posmatchc_pass.1.bin from 3759936288 to 3756337608
System memory: 50634444800
Mem2keepfree: 7595166720
Used by MIRA: 16477573120
Mem avail: 26561704960
rsh increased memtouse to: 26561704960
Edge vector capacity: 563719322
Can load up to 563714322 skim edges at once.
Partitioning into 2 blocks.
Blocks: 10360511 12389184
We have 630357946 skims in file.
Localtime: Wed Jul 23 22:27:40 2014
De-normalising SKIM hits ... (this will take a while)
Localtime: Wed Jul 23 22:28:33 2014
Localtime: Wed Jul 23 22:31:09 2014
Writing normalised skimblock 0 ( 16.0 GiB) ... done.
Localtime: Wed Jul 23 22:33:12 2014
Localtime: Wed Jul 23 22:33:35 2014
Writing normalised skimblock 10360511 ( 2.8 GiB) ... done.
Localtime: Wed Jul 23 22:33:40 2014
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Localtime: Wed Jul 23 22:35:19 2014
Step 0
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Localtime: Wed Jul 23 22:39:50 2014
Only short reads
Step 10
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 8237053
Step 20
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 248116023
Step 30
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 248116023
Step 40
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 248116023
Step 50
Total skims taken: 248116023
Step 53
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 279525419
Step 55
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 280994331
Step 56
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 281057837
Step 60
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Total skims taken: 281192824
Step solexa by critlevel
rsh4_takeSolexaByCritLevel.
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Taken 10934421 hits.
Step template overlaps
Loading block 0
Loading 536870783 elements at offset 0
Loaded 536870783 elements
Loading block 1
Loading 93487163 elements at offset 17179865056
Loaded 93487163 elements
Step NAO
rsh4_takeNeedAllOverlaps.
None needed.
Total skims taken: 292192873

Filtering forward skims.
Localtime: Wed Jul 23 22:57:16 2014
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Done.
Done.
Filtering complement skims.
Localtime: Wed Jul 23 22:58:15 2014
Writing reduced skim file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Done.
Done all filtering.
Localtime: Wed Jul 23 22:59:21 2014
Making alignments.
Localtime: Wed Jul 23 22:59:27 2014

Aligning possible forward matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Alignment stats:
Potential: 147051125
Calculated: 53074
Evaded (PB): 0
Rejected (checkfun): 0
Trans 100 saved: 146998051

Banned overlap pairs: 4127 in 2698 sets.

Localtime: Wed Jul 23 23:07:19 2014

Aligning possible complement matches:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Alignment stats:
Potential: 145141748
Calculated: 64936
Evaded (PB): 3
Rejected (checkfun): 0
Trans 100 saved: 145076809

Banned overlap pairs: 9109 in 5303 sets.

Localtime: Wed Jul 23 23:15:21 2014

Localtime: Wed Jul 23 23:15:21 2014
Counting number of alignments in file ... done.
Expecting 292183761 alignments.
Localtime: Wed Jul 23 23:16:43 2014
Loading confirmed 292183761 overlaps from disk (will need approximately 16.3 GiB RAM):
Ouch, out of memory detected.


========================== Memory self assessment ==============================
Running in 64 bit mode.

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 49447700 kB
MemFree: 139612 kB
Buffers: 1944 kB
Cached: 5967852 kB
SwapCached: 2588 kB
Active: 21693588 kB
Inactive: 27337208 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 49447700 kB
LowFree: 139612 kB
SwapTotal: 24579440 kB
SwapFree: 0 kB
Dirty: 3788 kB
Writeback: 0 kB
AnonPages: 43061204 kB
Mapped: 11812 kB
Slab: 62944 kB
PageTables: 156208 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 49303288 kB
Committed_AS: 69014976 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 276092 kB
VmallocChunk: 34359460459 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: 1389
Pid: 1389
PPid: 27991
TracerPid: 0
Uid: 506 506 506 506
Gid: 507 507 507 507
FDSize: 256
Groups: 100 507
VmPeak: 33724836 kB
VmSize: 33724828 kB
VmLck: 0 kB
VmHWM: 33544264 kB
VmRSS: 33543852 kB
VmData: 33664060 kB
VmStk: 92 kB
VmExe: 5524 kB
VmLib: 0 kB
VmPTE: 65584 kB
StaBrk: 05c62000 kB
Brk: 80a904000 kB
StaStk: 7fff0bf4c580 kB
Threads: 1
SigQ: 0/399360
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,ffffffff
Mems_allowed: 00000000,00000003
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 12389184 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 184 (184 B)

Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 12389184 47 MiB 0 B 0 B
AS_skim_edges: 0 16.8 GiB 16.8 GiB 0 B
AS_adsfacts: 0 24 B 0 B 0 B
AS_confirmed_edges: 0 24 B 0 B 0 B
AS_permanent_overlap_bans: 1 24 B 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: 12389184 47 MiB 0 B 0 B
AS_clipright: 12389184 47 MiB 0 B 0 B
AS_used_ids: 12389184 12 MiB 0 B 0 B
AS_multicopies: 12389184 12 MiB 0 B 0 B
AS_hasmcoverlaps: 0 12 MiB 12 MiB 0 B
AS_maxcoveragereached: 12389184 47 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 12389184 12 MiB 0 B 0 B
AS_isdebris: 12389184 12 MiB 0 B 0 B
AS_needalloverlaps: 12389184 12 MiB 0 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_usedtmpfiles: 25 816 B 0 B 0 B
Total: 18311582096 (17.1 GiB)

================================================================================


========================== Memory self assessment ==============================
Running in 64 bit mode.

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 49447700 kB
MemFree: 139004 kB
Buffers: 1976 kB
Cached: 5969012 kB
SwapCached: 2588 kB
Active: 21693604 kB
Inactive: 27338232 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 49447700 kB
LowFree: 139004 kB
SwapTotal: 24579440 kB
SwapFree: 0 kB
Dirty: 3788 kB
Writeback: 0 kB
AnonPages: 43061204 kB
Mapped: 11872 kB
Slab: 62900 kB
PageTables: 156208 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 49303288 kB
Committed_AS: 69014976 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 276092 kB
VmallocChunk: 34359460459 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------

Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 73%
Tgid: 1389
Pid: 1389
PPid: 27991
TracerPid: 0
Uid: 506 506 506 506
Gid: 507 507 507 507
FDSize: 256
Groups: 100 507
VmPeak: 33724836 kB
VmSize: 33724828 kB
VmLck: 0 kB
VmHWM: 33544264 kB
VmRSS: 33543924 kB
VmData: 33664060 kB
VmStk: 92 kB
VmExe: 5524 kB
VmLib: 0 kB
VmPTE: 65584 kB
StaBrk: 05c62000 kB
Brk: 80a904000 kB
StaStk: 7fff0bf4c580 kB
Threads: 1
SigQ: 0/399360
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed: 00000000,00000000,00000000,00000000,00000000,00000000,00000000,ffffffff
Mems_allowed: 00000000,00000003
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 12389184 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 184 (184 B)

Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 12389184 47 MiB 0 B 0 B
AS_skim_edges: 0 16.8 GiB 16.8 GiB 0 B
AS_adsfacts: 0 24 B 0 B 0 B
AS_confirmed_edges: 0 24 B 0 B 0 B
AS_permanent_overlap_bans: 1 24 B 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: 12389184 47 MiB 0 B 0 B
AS_clipright: 12389184 47 MiB 0 B 0 B
AS_used_ids: 12389184 12 MiB 0 B 0 B
AS_multicopies: 12389184 12 MiB 0 B 0 B
AS_hasmcoverlaps: 0 12 MiB 12 MiB 0 B
AS_maxcoveragereached: 12389184 47 MiB 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 12389184 12 MiB 0 B 0 B
AS_isdebris: 12389184 12 MiB 0 B 0 B
AS_needalloverlaps: 12389184 12 MiB 0 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_usedtmpfiles: 25 816 B 0 B 0 B
Total: 18311582096 (17.1 GiB)

================================================================================
Dynamic allocs: 4
Align allocs: 4
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.
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Old 07-24-2014, 04:12 AM   #11
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080
Default

You may have 48GB of RAM but are you able to use all of it? Are there any system wide limits enforced by your system administrators that are coming into play? Can you check the output of command below and make sure that it does not have limits on memory usage?

Quote:
$ limit
GenoMax is offline   Reply With Quote
Old 07-24-2014, 07:16 AM   #12
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

My feeling is that something else -- another program -- on the system is using your memory to the point where there is basically no memory left. You have 48 GB of ram and the maximum that Mira took up is 34GB with the current data structures around 20GB.

BTW: While we appreciate your faith in SeqAnswers answering your question, Bastian (mis-spelled) Chevreax is very good at answering questions. As the bottom of the output says:

Quote:
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
Send your output to him and he'll be able to give a definitive answer.
westerman is offline   Reply With Quote
Old 02-16-2015, 08:47 PM   #13
Nanu
Member
 
Location: New Delhi

Join Date: Sep 2014
Posts: 30
Default

Hi.,

I would like to denovo assembly of Ion torrent data. I am trying to use Mira., It ask for manifest file. May i have create the manifest file, if yes please let me know how to develop manifest file. 'coz its missing in mira folder.
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