[mira_talk] Re: Please consider
- From: monithamohan harilkumar <moniharil@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 16 May 2013 12:16:12 +0200
Hello Bastien,
Thanks for your quick response, it is indeed helpful, i have made mira to
run on resume option using -r , when I checked the log file until now(
However Mira is still running)...Can you please have a look at this log
file.(Just incase you find something unusual!!!I don't want to miss the
last option of running in Mira :))..Also Can you please tell me where to
check how much overlapping was done?
output /log file (.txt)
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 3.9.15 ().
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:
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To report bugs or ask for features, please use the new ticketing system at:
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This ensures that requests don't get lost.
Compiled by: bach
Thu Mar 28 01:37:42 CET 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 osa2 3.2.0-40-generic #64-Ubuntu SMP Mon Mar 25
21:22:10 UTC 2013 x86_64 x86_64 x86_
64 GNU/Linux
k: project
v: mira4
k: job
v: mapping,genome,accurate
k: parameters
v: -GE:not=32 COMMON_SETTINGS -AS:nop=1 -MI:somrnl=0 -SK:mnr=no:mmhr=1
SOLEXA_SETTINGS -CO:msr=no
k: readgroup
v: illuminaassembly
k: data
v: mira4_backbone_in.fna
k: as_reference
v:
k: strain
v: mira4_bft
k: parameters
v: COMMON_SETTINGS -DI:trt = /tmp2/tmp
k: default_qual
v: 30
k: readgroup
v: solexareads
k: data
v: /ctx/tmp1/monithesis/mira/mira3/mira4/mira41_in.solexa.fastq
/ctx/tmp1/monithesis/mira/mira3/mira4/mir
a42_in.solexa.fastq
k: technology
v: solexa
k: templatesize
v: 250 750 infoonly
k: segment_placement
v: ---> <--- infoonly
k: strain
v: mira4_sol
Readgroups after loading manifest:
RGI: 0 RGID: 0
RGN: UnassigneReads SN:
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 8 (UNDEFINED!!! SHOULD NEVER BE SEEN) namschem: 0 SID: 0
DQ: 212
BB: 0 Rail: 0 CER: 0
RGI: 1 RGID: 1
RGN: illuminaassembly SN: mira4_bft
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 5 (Text) namschem: 6 SID: 0
DQ: 30
BB: 1 Rail: 0 CER: 0
RGI: 2 RGID: 2
RGN: solexareads SN: mira4_sol
SP: ---> <--- SPio: 1 SPC: -1 IF: 250 IT: 750 TSio: 1
ST: 6 (Solexa) namschem: 4 SID: 0
DQ: 30
BB: 0 Rail: 0 CER: 0
Looking for files named in data ...Pushing back filename:
"mira4_backbone_in.fna"
Pushing back filename:
"/ctx/tmp1/monithesis/mira/mira3/mira4/mira41_in.solexa.fastq"
Pushing back filename:
"/ctx/tmp1/monithesis/mira/mira3/mira4/mira42_in.solexa.fastq"
Manifest:
projectname: mira4
job: mapping,genome,accurate
parameters: -GE:not=32 COMMON_SETTINGS -AS:nop=1 -MI:somrnl=0
-SK:mnr=no:mmhr=1 SOLEXA_SETTINGS -CO:msr=no
COMMON_SETTINGS -DI:trt = /tmp2/tmp
Manifest load entries: 2
MLE 1:
RGID: 1
RGN: illuminaassembly SN: mira4_bft
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 5 (Text) namschem: 6 SID: 0
DQ: 30
BB: 1 Rail: 0 CER: 0
mira4_backbone_in.fna MLE 2:
RGID: 2
RGN: solexareads SN: mira4_sol
SP: ---> <--- SPio: 1 SPC: -1 IF: 250 IT: 750 TSio: 1
ST: 6 (Solexa) namschem: 4 SID: 0
DQ: 30
BB: 0 Rail: 0 CER: 0
/ctx/tmp1/monithesis/mira/mira3/mira4/mira41_in.solexa.fastq
/ctx/tmp1/monithesis/mira/mira3/mira4/mira42_
in.solexa.fastq
Seen parameters in manifest: --job=mapping,genome,accurate,Solexa
-GE:not=32 COMMON_SETTINGS -AS:nop=1 -MI
:somrnl=0 -SK:mnr=no:mmhr=1 SOLEXA_SETTINGS -CO:msr=no COMMON_SETTINGS
-DI:trt = /tmp2/tmp
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), Solexa data
Used parameter settings:
General (-GE):
Project name : mira4
Number of threads (not) : 32
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) : [san] yes
[sxa] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 1
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 1
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [san] 80
[sxa] 20
Minimum reads per contig (mrpc) : [san] 2
[sxa] 10
Enforce presence of qualities (epoq) : [san] yes
[sxa] yes
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[sxa] 2
Minimum length (ardml) : [san] 400
[sxa] 200
Grace length (ardgl) : [san] 40
[sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [san] 1.5
[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) : 0
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) : no
Dataprocessing options (-DP):
Use read extensions (ure) : [san] yes
[sxa] no
Read extension window length (rewl) : [san] 30
[sxa] 30
Read extension w. maxerrors (rewme) : [san] 2
[sxa] 2
First extension in pass (feip) : [san] 0
[sxa] 0
Last extension in pass (leip) : [san] 0
[sxa] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [san] 10
[sxa] 1
Max front gap (msvsmfg) : [san] 60
[sxa] 2
Max end gap (msvsmeg) : [san] 120
[sxa] 2
Strict front clip (msvssfc) : [san] 0
[sxa] 0
Strict end clip (msvssec) : [san] 0
[sxa] 0
Possible vector leftover clip (pvlc) : [san] yes
[sxa] no
maximum len allowed (pvcmla) : [san] 18
[sxa] 18
Min qual. threshold for entire read (mqtfer): [san] 0
[sxa] 0
Number of bases (mqtfernob) : [san] 0
[sxa] 15
Quality clip (qc) : [san] no
[sxa] no
Minimum quality (qcmq) : [san] 20
[sxa] 20
Window length (qcwl) : [san] 30
[sxa] 30
Bad stretch quality clip (bsqc) : [san] yes
[sxa] no
Minimum quality (bsqcmq) : [san] 20
[sxa] 5
Window length (bsqcwl) : [san] 30
[sxa] 20
Masked bases clip (mbc) : [san] yes
[sxa] no
Gap size (mbcgs) : [san] 20
[sxa] 5
Max front gap (mbcmfg) : [san] 40
[sxa] 12
Max end gap (mbcmeg) : [san] 60
[sxa] 12
Lower case clip front (lccf) : [san] no
[sxa] no
Lower case clip back (lccb) : [san] no
[sxa] no
Clip poly A/T at ends (cpat) : [san] no
[sxa] no
Keep poly-a signal (cpkps) : [san] no
[sxa] no
Minimum signal length (cpmsl) : [san] 12
[sxa] 12
Max errors allowed (cpmea) : [san] 1
[sxa] 1
Max gap from ends (cpmgfe) : [san] 9
[sxa] 9
Clip 3 prime polybase (c3pp) : [san] no
[sxa] yes
Minimum signal length (c3ppmsl) : [san] 12
[sxa] 12
Max errors allowed (c3ppmea) : [san] 2
[sxa] 2
Max gap from ends (c3ppmgfe) : [san] 9
[sxa] 9
Clip known adaptors right (ckar) : [san] no
[sxa] yes
Ensure minimum left clip (emlc) : [san] yes
[sxa] no
Minimum left clip req. (mlcr) : [san] 25
[sxa] 0
Set minimum left clip to (smlc) : [san] 30
[sxa] 0
Ensure minimum right clip (emrc) : [san] no
[sxa] no
Minimum right clip req. (mrcr) : [san] 10
[sxa] 10
Set minimum right clip to (smrc) : [san] 20
[sxa] 20
Apply SKIM chimera detection clip (ascdc) : no
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : [san] yes
[sxa] yes
Bases per hash (pecbph) : 31
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [san] 1
[sxa] 0
Back freq (pbfreq) : [san] 1
[sxa] 0
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [san] no
[sxa] yes
Back forward-rev (pbfore) : [san] no
[sxa] yes
Front conf. multi-seq type (pfcmst) : [san] no
[sxa] yes
Back conf. multi-seq type (pbcmst) : [san] no
[sxa] yes
Front seen at low pos (pfsalp) : [san] no
[sxa] no
Back seen at low pos (pbsalp) : [san] no
[sxa] no
Clip bad solexa ends (cbse) : [san] no
[sxa] yes
Rare kmer mask (rkm) : [san] 0
[sxa] 0
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 32
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 10
Hash save stepping (hss) : 1
Percent required (pr) : [san] 60
[sxa] 60
Max hits per read (mhpr) : 2000
Max megahub ratio (mmhr) : 1
SW check on backbones (swcob) : yes
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) : no
Nasty repeat ratio (nrr) : 100
Repeat level in info file (rliif) : 6
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 4096
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[sxa] yes
Quick rule min len 1 (qrml1) : [san] 200
[sxa] -90
Quick rule min sim 1 (qrms1) : [san] 90
[sxa] 100
Quick rule min len 2 (qrml2) : [san] 100
[sxa] -80
Quick rule min sim 2 (qrms2) : [san] 95
[sxa] 100
Backbone quick overlap min len (bqoml) : [san] 150
[sxa] 20
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[sxa] 20
Bandwidth max (bmax) : [san] 130
[sxa] 80
Bandwidth min (bmin) : [san] 25
[sxa] 20
Minimum score (ms) : [san] 30
[sxa] 15
Minimum overlap (mo) : [san] 17
[sxa] 20
Minimum relative score in % (mrs) : [san] 70
[sxa] 60
Solexa_hack_max_errors (shme) : [san] -1
[sxa] -1
Extra gap penalty (egp) : [san] no
[sxa] no
extra gap penalty level (egpl) : [san] low
[sxa] low
Max. egp in percent (megpp) : [san] 100
[sxa] 100
Contig parameters (-CO):
Name prefix (np) : mira4
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[sxa] 30
Mark repeats (mr) : yes
Only in result (mroir) : yes
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[sxa] 3
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[sxa] 30
End-read Marking Exclusion Area in bases (emea) : [san] 1
[sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[sxa] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[sxa] no
Merge short reads (msr) : [san] no
[sxa] no
Max errors (msrme) : [san] 0
[sxa] 0
Keep ends unmerged (msrkeu) : [san] -1
[sxa] -1
Gap override ratio (gor) : [san] 66
[sxa] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[sxa] no
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) : 0
Extra flag 1 / sanity track check (ef1) : yes
Extra flag 2 / dnredreadsatpeaks (ef2) : yes
Directories (-DI):
Working directory :
Top directory for writing files : mira4_assembly
For writing result files : mira4_assembly/mira4_d_results
For writing result info files : mira4_assembly/mira4_d_info
For writing tmp files : /tmp2/tmp/mira4_d_tmp
Tmp redirected to (trt) : /tmp2/tmp
For writing checkpoint files : mira4_assembly/mira4_d_chkpt
File names (-FN):
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[sxa] no
Save tagged singlets in project (stsip) : [san] yes
[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 : mira4_out.caf
MAF : mira4_out.maf
FASTA : mira4_out.unpadded.fasta
FASTA quality : mira4_out.unpadded.fasta.qual
FASTA (padded) : mira4_out.padded.fasta
FASTA qual.(pad): mira4_out.padded.fasta.qual
GAP4 (directory): mira4_out.gap4da
ACE : mira4_out.ace
HTML : mira4_out.html
Simple text : mira4_out.txt
TCS overview : mira4_out.tcs
Wiggle : mira4_out.wig
------------------------------------------------------------------------------
Deleting old directory mira4_assembly/mira4_d_results ... done.
Creating directory mira4_assembly/mira4_d_results ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Wed May 15 12:21:09 2013
Loading MAF mira4_assembly/mira4_d_chkpt/readpool.maf :
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|..tcmalloc: lar
ge alloc 1073741824 bytes == 0x100896c000 @
.. [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....tcmalloc:
large alloc 1342177280 bytes == 0x1
9b175c000 @
|.... [100%]
Localtime: Wed May 15 12:36:31 2013
tcmalloc: large alloc 2779873280 bytes == 0x1c48a58000 @
tcmalloc: large alloc 2779873280 bytes == 0x1c48a58000 @
Generated 59578260 unique DNA template ids for 115827946 valid reads.
Tmp directory is not on a NFS mount, good.
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
Tgid: 28121
Pid: 28121
PPid: 17549
TracerPid: 0
Uid: 1017 1017 1017 1017
Gid: 1001 1001 1001 1001
FDSize: 256
Groups: 100 1001
VmPeak: 123142124 kB
VmSize: 123142124 kB
VmLck: 0 kB
VmPin: 0 kB
VmHWM: 120558716 kB
VmRSS: 120558480 kB
VmData: 123133624 kB
VmStk: 136 kB
VmExe: 5468 kB
VmLib: 0 kB
VmPTE: 235524 kB
VmSwap: 0 kB
Threads: 1
SigQ: 0/4127291
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000001
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed: ffffffff,ffffffff
Cpus_allowed_list: 0-63
Mems_allowed: 00000000,000000ff
Mems_allowed_list: 0-7
voluntary_ctxt_switches: 183
nonvoluntary_ctxt_switches: 137506
--------------------------------------------------------------------------------
Pass: 1 / 1
===========================================================================
Pool statistics:
Backbones: 12 Backbone rails: 3328562
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 112499372 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 110880498 0
Avg tot rlen 0 0 0 0 0 0 100 0
Avg rlen used 0 0 0 0 0 0 92 0
With strain 0 0 0 0 0 0 112499372 0
W/o clips 0 0 0 0 0 0 108428807 0
Sanger total bases:0 used bases in used reads: 0
454 total bases:0 used bases in used reads: 0
IonTor total bases:0 used bases in used reads: 0
PcBioHQ total bases:0 used bases in used reads: 0
PcBioLQ total bases:0 used bases in used reads: 0
Text total bases:0 used bases in used reads: 0
Solexa total bases:11249937200 used bases in used reads: 10240180452
Solid total bases:0 used bases in used reads: 0
===========================================================================
Localtime: Wed May 15 12:41:43 2013
Writing temporary hstat files:
freemem: 398902419456
TNH: 9242421128
XME 1: 367.261
XME 2: 16
NEPB 1: 16777216
NEPB 2: 16777216
[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 May 15 14:16:46 2013
Analysing hstat files:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....
|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Localtime: Wed May 15 14:16:47 2013
clean up temporary stat files...Localtime: Wed May 15 14:16:47 2013
Localtime: Wed May 15 14:16:47 2013
Hash statistics:
=========================================================
Measured avg. frequency coverage: 21119
Deduced thresholds:
-------------------
Min normal cov: 8447.6
Max normal cov: 33790.4
Repeat cov: 40126.1
Heavy cov: 168952
Crazy cov: 422380
Mask cov: 2111900
Repeat ratio histogram:
-----------------------
0 437184
1 461031
2 96626
3 28764
4 11209
5 5508
6 2937
7 1672
8 1079
9 658
10 415
11 342
12 246
13 186
14 152
15 105
16 86
17 61
18 64
19 30
20 28
21 24
22 25
23 11
24 14
25 8
26 9
27 4
28 4
30 5
31 8
32 2
33 4
34 6
35 6
36 6
37 8
39 8
40 2
42 4
43 2
44 6
45 2
46 2
50 2
52 1
53 4
54 4
55 2
60 2
68 2
70 2
75 2
110 2
=========================================================
Assigning statistics values:
Localtime: Wed May 15 14:16:47 2013
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....
|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
Localtime: Wed May 15 15:08:51 2013
Buntifying reads (this may take a while) ... done.
Writing read repeat info to:
mira4_assembly/mira4_d_info/mira4_info_readrepeats.lst ... 64346 sequences
wi
th 73694 masked stretches.
AS_resumeasembly 1
AS_resumeisok 1
fileExists(/tmp2/tmp/mira4_d_tmp/mira4_signal_findpossibleoverlaps_pass.1.ok)
0
Localtime: Wed May 15 15:15:24 2013
Searching for possible overlaps (only against backbone, the progress bar
will be skewed):
Localtime: Wed May 15 15:15:24 2013
Now running threaded and partitioned skimmer with 734 partitions in 32
threads:
[0%] truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
35716186008 to 35716186008
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchc_pass.1.bin from
35619238752 to 35619238752
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
73412592672 to 73412592672
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchc_pass.1.bin from
73140536640 to 73140536640
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
111735437472 to 111735437472
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchc_pass.1.bin from
111411991416 to 111411991416
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
148070679312 to 148070679312
.truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchc_pass.1.bin from
147703855176 to 147703855176
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
181213417440 to 181213417440
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchc_pass.1.bin from
180794488608 to 180794488608
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
215099212584 to 215099212584
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchc_pass.1.bin from
214611191136 to 214611191136
truncating /tmp2/tmp/mira4_d_tmp/mira4_int_posmatchf_pass.1.bin from
250617768576 to 250617768576
Thanks and regards,
Monitha MOhan
On Wed, May 15, 2013 at 11:22 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
> On May 15, 2013, at 15:23 , monithamohan harilkumar <moniharil@xxxxxxxxx>
> wrote:
> > Thanks for your response, But MY doubt is , it kind of generated 2
> terabyte of tmp files, its expected to get full disk then..!!!!
> > I am trying to do mapping with paired end data where each file of paired
> end is 13G and and my backbone file from oryza (reference) is 373M.The tmp
> directory created in mira are
>
> I feel your pain.It might have been helpful for you to note how many
> percent the overlap search was done when it stopped because of full disk.
> One could have made a guess how much space in total would be required.
>
> It looks like mapping of short reads to higher eukaryotes is not well
> optimised in MIRA, especially if they contain lots of repeats. There is
> nothing you can do except provide more disk space. In the end it might very
> well be that you need to resort to other programs.
>
> >
> > -rw-r--r-- 1 monitha ctx 3736931776 May 1 01:36
> mira4_int_clippings.0.txt
> > -rw-r--r-- 1 monitha ctx 6882733 Apr 30 14:00
> mira4_int_clippings_t0.0.txt
>
> If you want to recover a bit of disk space, you can delete/move away the
> *clippings* files: they just contain text info on what MIRA clipped where
> and why in your reads.
>
> Sorry not to have better news,
> Bastien
>
>
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