[mira_talk] Re: Help
- From: "Raj Kumar, Praveen Kumar Mr." <rajkump@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 6 Aug 2010 17:49:16 -0400
Dear Bastein,
Log file is attached.
Thank you,
Praveen
______________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On Behalf
Of Bastien Chevreux [bach@xxxxxxxxxxxx]
Sent: Friday, August 06, 2010 5:30 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Help
Can you please send the whole log?
----- original Nachricht --------
Betreff: [mira_talk] Re: Help
Gesendet: Fr, 06. Aug 2010
Von: Raj Kumar, Praveen Kumar Mr.<rajkump@xxxxxxxxxx>
> Dear Bastein,
> I am sorry to let you know this, I still the error msg.
>
>
> CMD:/software/mira/mira_3.2.0rc3_dev_linux-gnu_x86_64_static/bin/mira
> --project=EAch --job=est,denovo,accurate,sanger,454 SANGER_SETTINGS
> -CL:qc=no 454_SETTINGS -LR:mxti=no -AL:mrs=95 -CO:rodirs=5 COMMON_SETTINGS
> -SK:mnr=yes:nrr=10 -MI:sonfs=false >& log_assembly.txt
>
> ****************************************************************************
> *****************
> WARNING WARNING WARNING!
>
> It looks like the log directory is on a NFS mount. This will slow down MIRA
> *considerably* ... by about a factor of 10!
> If you don't want that, you have three possibilities:
>
> 1) RECOMMENDED! Use -DI:lrt to redirect the log directory somewhere else on
> a
> local disk or even SSD.
> 2) POSSIBLE: put the whole project somewhere else and restart MIRA.
> 3) ABSOLUTELY NOT RECOMMENDED AT ALL: use -MI:sonfs=false to tell MIRA not
> to stop when it finds the log directory on NFS.
>
>
> Fatal error (may be due to problems of the input data or parameters):
>
> "Log directory is on a NFS mount ... but we don't want that."
>
> ->Thrown: void Assembly::checkForNFSMountOnLogDir()
> ->Caught: main
>
> Aborting process, probably due to error in the input data or
> parametrisation.
> Please check the output log for more information.
> For help, please write a mail to the mira talk mailing list.
>
> CWD: /shared/liangcres/cdna3055.assembly
> Thank you for noticing that this is *NOT* a crash, but a
> controlled program stop.
> *************************************************************
>
> regards,
> Praveen
> ________________________________________
> From: mira_talk-bounce@xxxxxxxxxxxxx [mira_talk-bounce@xxxxxxxxxxxxx] On
> Behalf Of Bastien Chevreux [bach@xxxxxxxxxxxx]
> Sent: Friday, August 06, 2010 1:31 PM
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: Help
>
> On Donnerstag 05 August 2010 Raj Kumar, Praveen Kumar Mr. wrote:
> > Dear Bob,
> > I followed suggestion #3 and I still get the following error msg,
>
> Yikes. I really need some vacation ... failing to implement such an easy
> parameter is not a good sign.
>
> Anyway.
>
> Praveen, there's a 64 bit hot-fix binary here which should fix your
> problem:
>
> http://www.chevreux.org/tmp/mira.bz2
>
> Please tell if it does.
>
> B.
>
>
> --
> 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
>
> --
> 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
>
--- original Nachricht Ende ----
--
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
This is MIRA V3.2.0rc3 (development version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
To (un-)subscribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
After subscribing, mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
To report bugs or ask for features, please use the new ticketing system at:
http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.
Compiled by: bach
Sat Jul 31 14:54:28 CEST 2010
On: Linux arcadia64 2.6.27-11-generic #1 SMP Wed Apr 1 20:53:41 UTC 2009 x86_64
GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compilation 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 compute-0-0.local 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17
11:30:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=EAch --job=est,denovo,accurate,sanger,454
SANGER_SETTINGS -CL:qc=no 454_SETTINGS -LR:mxti=no -AL:mrs=95 -CO:rodirs=5
COMMON_SETTINGS -SK:mnr=yes:nrr=10 -MI:sonfs=false
Parameters parsed without error, perfect.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), 454 data
Used parameter settings:
General (-GE):
Project name in (proin) : EAch
Project name out (proout) : EAch
Number of threads (not) : 2
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
Keep contigs in memory (kcim) : no
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
[454] yes
Template insert size minimum (tismin) : [san] -1
[454] -1
Template insert size maximum (tismax) : [san] -1
[454] -1
Template partner build direction (tpbd) : [san] -1
[454] -1
Colour reads by hash frequency (crhf) : no
Load reads options (-LR):
Load sequence data (lsd) : [san] yes
[454] yes
File type (ft) : [san] fasta
[454] fasta
External quality (eq) : from SCF (scf)
Ext. qual. override (eqo) : no
Discard reads on e.q. error (droeqe): no
Solexa scores in qual file (ssiqf) : no
FASTQ qual offset (fqqo) : [san] 0
[454] 0
Wants quality file (wqf) : [san] yes
[454] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[454] forward/reverse
(fr)
Merge with XML trace info (mxti) : [san] no
[454] no
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 5
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 3
Minimum read length (mrl) : [san] 80
[454] 40
Minimum reads per contig (mrpc) : [san] 2
[454] 2
Base default quality (bdq) : [san] 10
[454] 10
Enforce presence of qualities (epoq) : [san] yes
[454] yes
Automatic repeat detection (ard) : no
Coverage threshold (ardct) : [san] 2
[454] 2
Minimum length (ardml) : [san] 400
[454] 200
Grace length (ardgl) : [san] 40
[454] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 4
Cutoff multiplier (urdcm) : [san] 1.5
[454] 1.5
Keep long repeats separated (klrs) : no
Spoiler detection (sd) : 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) : 3600
Strain and backbone options (-SB):
Load straindata (lsd) : no
Load backbone (lb) : no
Start backbone usage in pass (sbuip) : 3
Backbone file type (bft) : fasta
Backbone base quality (bbq) : 30
Backbone strain name (bsn) :
Force for all (bsnffa) : no
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Also build new contigs (abnc) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [san] no
[454] no
Read extension window length (rewl) : [san] 30
[454] 15
Read extension w. maxerrors (rewme) : [san] 2
[454] 2
First extension in pass (feip) : [san] 0
[454] 0
Last extension in pass (leip) : [san] 0
[454] 0
Clipping options (-CL):
Merge with SSAHA vector screen (msvs) : [san] no
[454] no
Gap size (msvsgs) : [san] 10
[454] 8
Max front gap (msvsmfg) : [san] 60
[454] 8
Max end gap (msvsmeg) : [san] 120
[454] 12
Strict front clip (msvssfc) : [san] 0
[454] 0
Strict end clip (msvssec) : [san] 0
[454] 0
Possible vector leftover clip (pvlc) : [san] no
[454] no
maximum len allowed (pvcmla) : [san] 18
[454] 18
Quality clip (qc) : [san] no
[454] no
Minimum quality (qcmq) : [san] 20
[454] 20
Window length (qcwl) : [san] 30
[454] 30
Bad stretch quality clip (bsqc) : [san] no
[454] no
Minimum quality (bsqcmq) : [san] 20
[454] 5
Window length (bsqcwl) : [san] 30
[454] 20
Masked bases clip (mbc) : [san] yes
[454] yes
Gap size (mbcgs) : [san] 20
[454] 5
Max front gap (mbcmfg) : [san] 40
[454] 12
Max end gap (mbcmeg) : [san] 60
[454] 12
Lower case clip (lcc) : [san] no
[454] yes
Clip poly A/T at ends (cpat) : [san] yes
[454] yes
Keep poly-a signal (cpkps) : [san] no
[454] no
Minimum signal length (cpmsl) : [san] 12
[454] 12
Max errors allowed (cpmea) : [san] 1
[454] 1
Max gap from ends (cpmgfe) : [san] 20000
[454] 20000
Ensure minimum left clip (emlc) : [san] no
[454] no
Minimum left clip req. (mlcr) : [san] 25
[454] 4
Set minimum left clip to (smlc) : [san] 30
[454] 4
Ensure minimum right clip (emrc) : [san] no
[454] no
Minimum right clip req. (mrcr) : [san] 10
[454] 10
Set minimum right clip to (smrc) : [san] 20
[454] 15
Apply SKIM chimera detection clip (ascdc) : no
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : no
Bases per hash (pecbph) : 17
Handle Solexa GGCxG problem (pechsgp) : yes
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 2
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 21
Hash save stepping (hss) : 1
Percent required (pr) : [san] 70
[454] 80
Max hits per read (mhpr) : 30
Max megahub ratio (mmhr) : 0
Freq. est. min normal (fenn) : 0.4
Freq. est. max normal (fexn) : 1.6
Freq. est. repeat (fer) : 1.9
Freq. est. heavy repeat (fehr) : 8
Freq. est. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 10
Repeat level in info file (rliif) : 6
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 2048
Pathfinder options (-PF):
Use quick rule (uqr) : [san] yes
[454] yes
Quick rule min len 1 (qrml1) : [san] 200
[454] 80
Quick rule min sim 1 (qrms1) : [san] 90
[454] 90
Quick rule min len 2 (qrml2) : [san] 100
[454] 60
Quick rule min sim 2 (qrms2) : [san] 95
[454] 95
Backbone quick overlap min len (bqoml) : [san] 150
[454] 80
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 20
[454] 20
Bandwidth max (bmax) : [san] 130
[454] 80
Bandwidth min (bmin) : [san] 25
[454] 20
Minimum score (ms) : [san] 30
[454] 15
Minimum overlap (mo) : [san] 15
[454] 20
Minimum relative score in % (mrs) : [san] 85
[454] 95
Solexa_hack_max_errors (shme) : [san] 0
[454] 0
Extra gap penalty (egp) : [san] yes
[454] yes
extra gap penalty level (egpl) : [san] reject_codongaps
[454] reject_codongaps
Max. egp in percent (megpp) : [san] 100
[454] 100
Contig parameters (-CO):
Name prefix (np) : EAch
Reject on drop in relative alignment score in % (rodirs) : [san] 10
[454] 5
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [san] 2
[454] 4
Minimum neighbour quality needed for tagging (mnq) : [san] 20
[454] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
[454] 25
End-read Marking Exclusion Area in bases (emea) : [san] 25
[454] 10
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [san] yes
[454] no
Also mark gap bases - even multicolumn (amgbemc) : [san] yes
[454] yes
Also mark gap bases - need both strands (amgbnbs): [san] yes
[454] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
[454] no
Merge short reads (msr) : [san] no
[454] no
Gap override ratio (gor) : [san] 66
[454] 66
Edit options (-ED):
Automatic contig editing (ace) : [san] no
[454] yes
Sanger only:
Strict editing mode (sem) : no
Confirmation threshold in percent (ct) : 50
Misc (-MI):
Stop on NFS (sonfs) : yes
Directories (-DI):
When loading EXP files :
When loading SCF files :
Top directory for writing files : EAch_assembly
For writing result files : EAch_assembly/EAch_d_results
For writing result info files : EAch_assembly/EAch_d_info
For writing log files : EAch_assembly/EAch_d_log
Log redirected to (lrt) :
For writing checkpoint files : EAch_assembly/EAch_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
EAch_in.sanger.fasta
[454] EAch_in.454.fasta
When loading qualities from FASTA quality : [san]
EAch_in.sanger.fasta.qual
[454]
EAch_in.454.fasta.qual
When loading sequences from FASTQ : [san]
EAch_in.sanger.fastq
[454] EAch_in.454.fastq
When loading project from CAF : EAch_in.sanger.caf
When loading project from MAF (disabled) : EAch_in.sanger.maf
When loading EXP fofn : EAch_in.sanger.fofn
When loading project from PHD : EAch_in.phd.1
When loading strain data : EAch_straindata_in.txt
When loading XML trace info files : [san]
EAch_traceinfo_in.sanger.xml
[454]
EAch_traceinfo_in.454.xml
When loading SSAHA vector screen results :
EAch_ssaha2vectorscreen_in.txt
When loading backbone from MAF : EAch_backbone_in.maf
When loading backbone from CAF : EAch_backbone_in.caf
When loading backbone from GenBank : EAch_backbone_in.gbf
When loading backbone from FASTA : EAch_backbone_in.fasta
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [san] no
[454] no
Save tagged singlets in project (stsip) : [san] yes
[454] yes
Remove rollover logs (rrol) : yes
Remove log directory (rld) : no
Result files:
Saved as CAF (orc) : yes
Saved as FASTA (orf) : yes
Saved as GAP4 (directed assembly) (org) : no
Saved as phrap ACE (ora) : yes
Saved as HTML (orh) : no
Saved as Transposed Contig Summary (ors) : yes
Saved as simple text format (ort) : no
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 : EAch_out.caf
MAF : EAch_out.maf
FASTA : EAch_out.unpadded.fasta
FASTA quality : EAch_out.unpadded.fasta.qual
FASTA (padded) : EAch_out.padded.fasta
FASTA qual.(pad): EAch_out.padded.fasta.qual
GAP4 (directory): EAch_out.gap4da
ACE : EAch_out.ace
HTML : EAch_out.html
Simple text : EAch_out.txt
TCS overview : EAch_out.tcs
Wiggle : EAch_out.wig
------------------------------------------------------------------------------
Creating directory EAch_assembly ... done.
Creating directory EAch_assembly/EAch_d_log ... done.
Creating directory EAch_assembly/EAch_d_results ... done.
Creating directory EAch_assembly/EAch_d_info ... done.
Creating directory EAch_assembly/EAch_d_chkpt ... done.
WARNING WARNING WARNING!
It looks like the log directory is on a NFS mount. This will slow down MIRA
*considerably* ... by about a factor of 10!
If you don't want that, you have three possibilities:
1) RECOMMENDED! Use -DI:lrt to redirect the log directory somewhere else on a
local disk or even SSD.
2) POSSIBLE: put the whole project somewhere else and restart MIRA.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use -MI:sonfs=false to tell MIRA not
to stop when it finds the log directory on NFS.
Fatal error (may be due to problems of the input data or parameters):
"Log directory is on a NFS mount ... but we don't want that."
->Thrown: void Assembly::checkForNFSMountOnLogDir()
->Caught: main
Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
CWD: /shared/liangcres/cdna3055.assembly
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Other related posts:
