[mira_talk] Re: Solexa seq assembly
- From: "Ragupathy, Raja " <Raja.Ragupathy@xxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 30 Mar 2010 15:54:15 -0400
Thanks Jeremiah and Bastien for suggestions.
Still it didn't work.
Hi Bastien, since the output log folder is empty, I am attaching the output
from the monitor as an attachment.
Thanks again.
Raja
Raja Ragupathy PhD,
Post-Doctoral Fellow
Genomics and Sequencing labs,
AAFC-Cereal Research Centre
Winnipeg, Manitoba
Canada R3T2M9
Phone: 204-983 8194
E-mail: ragupathyr@xxxxxxxxx
-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Bastien Chevreux
Sent: March 29, 2010 5:38 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Solexa seq assembly
On Montag 29 März 2010 Ragupathy, Raja wrote:
> I just started working with Mira. When I want to do denovo genome
> assembly of solexa short reads (fastq files), MIRA gives the error
> message-'program aborted due to error in input data or parametrisation.
> Could you please advice?
Can you please post the complete output log?
Regards,
Bastien
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tbanks@mbwinnr502727:~/Downloads/mira/bin$ ./mira -project=Lu000z
-job=denovo,genome,draft,solexa SOLEXA_SETTINGS -AS:epoq=no -AS:mrl=20
This is MIRA V3.0.3 (production version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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Compiled by: bach
Sat Mar 13 10:04:34 CET 2010
On: Linux varcadia32 2.6.27-11-generic #1 SMP Thu Jan 29 19:24:39 UTC 2009 i686
GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compilation settings (sorry, for debug):
Size of size_t : 4
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux mbwinnr502727 2.6.27-11-generic #1 SMP Wed Apr 1 20:57:48
UTC 2009 i686 GNU/Linux
Parsing parameters: -project=Lu000z -job=denovo,genome,draft,solexa
SOLEXA_SETTINGS -AS:epoq=no -AS:mrl=20
-SB:sbuip is 3, but must be no more than 1. Setting to 1
Parameters parsed without error, perfect.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), Solexa data
Used parameter settings:
General (-GE):
Project name in (proin) : Lu000z
Project name out (proout) : Lu000z
Number of threads (not) : 2
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 10
Max. process size (mps) : 0
Keep contigs in memory (kcim) : no
EST SNP pipeline step (esps) : 1
Use template information (uti) : [san] yes
[sxa] yes
Template insert size minimum (tismin): [san] -1
[sxa] -1
Template insert size maximum (tismax): [san] -1
[sxa] -1
Colour reads by hash frequency (crhf) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] no
[sxa] yes
File type (ft) : [san] fasta
[sxa] fastq
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
[sxa] 0
Wants quality file (wqf) : [san] yes
[sxa] yes
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[sxa] Solexa (solexa)
Merge with XML trace info (mxti) : [san] no
[sxa] no
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
Minimum read length (mrl) : [san] 80
[sxa] 20
Base default quality (bdq) : [san] 10
[sxa] 10
Enforce presence of qualities (epoq) : [san] yes
[sxa] no
Automatic repeat detection (ard) : yes
Coverage threshold (ardct) : [san] 2
[sxa] 2.5
Minimum length (ardml) : [san] 400
[sxa] 300
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) : no
Last pass only (sdlpo) : yes
Use genomic pathfinder (ugpf) : yes
Use emergency search stop (uess) : yes
ESS partner depth (esspd) : 500
Use emergency blacklist (uebl) : yes
Use max. contig build time (umcbt) : no
Build time in seconds (bts) : 10000
Strain and backbone options (-SB):
Load straindata (lsd) : no
Load backbone (lb) : no
Start backbone usage in pass (sbuip) : 1
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
[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):
Merge with SSAHA vector screen (msvs) : [san] no
[sxa] no
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] no
[sxa] no
maximum len allowed (pvcmla) : [san] 18
[sxa] 18
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 (lcc) : [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
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) : yes
Apply SKIM junk detection clip (asjdc) : yes
Propose end clips (pec) : yes
Bases per hash (pecbph) : 21
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 2
Bases per hash (bph) : 17
Hash save stepping (hss) : 4
Percent required (pr) : [san] 70
[sxa] 90
Max hits per read (mhpr) : 200
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) : 100
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] 33
Quick rule min sim 1 (qrms1) : [san] 90
[sxa] 100
Quick rule min len 2 (qrml2) : [san] 100
[sxa] 30
Quick rule min sim 2 (qrms2) : [san] 95
[sxa] 100
Backbone quick overlap min len (bqoml) : [san] 150
[sxa] 20
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [san] 15
[sxa] 20
Bandwidth max (bmax) : [san] 70
[sxa] 80
Bandwidth min (bmin) : [san] 25
[sxa] 20
Minimum score (ms) : [san] 30
[sxa] 15
Minimum overlap (mo) : [san] 15
[sxa] 25
Minimum relative score in % (mrs) : [san] 65
[sxa] 90
Solexa_hack_max_errors (shme) : [san] 0
[sxa] 0
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) : Lu000z
Reject on drop in relative alignment score in % (rodirs) : [san] 15
[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) : [san] 2
[sxa] 4
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] 25
[sxa] 4
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
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
Directories (-DI):
When loading EXP files :
When loading SCF files :
Top directory for writing files : Lu000z_assembly
For writing result files : Lu000z_assembly/Lu000z_d_results
For writing result info files : Lu000z_assembly/Lu000z_d_info
For writing log files : Lu000z_assembly/Lu000z_d_log
For writing checkpoint files : Lu000z_assembly/Lu000z_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
Lu000z_in.sanger.fasta
[sxa]
Lu000z_in.solexa.fasta
When loading qualities from FASTA quality : [san]
Lu000z_in.sanger.fasta.qual
[sxa]
Lu000z_in.solexa.fasta.qual
When loading sequences from FASTQ : [san]
Lu000z_in.sanger.fastq
[sxa]
Lu000z_in.solexa.fastq
When loading project from CAF : Lu000z_in.sanger.caf
When loading project from MAF (disabled) : Lu000z_in.sanger.maf
When loading EXP fofn : Lu000z_in.fofn
When loading project from PHD : Lu000z_in.phd.1
When loading strain data : Lu000z_straindata_in.txt
When loading XML trace info files : [san]
Lu000z_traceinfo_in.sanger.xml
[sxa]
Lu000z_traceinfo_in.solexa.xml
When loading SSAHA vector screen results :
Lu000z_ssaha2vectorscreen_in.txt
When loading backbone from MAF : Lu000z_backbone_in.maf
When loading backbone from CAF : Lu000z_backbone_in.caf
When loading backbone from GenBank : Lu000z_backbone_in.gbf
When loading backbone from FASTA : Lu000z_backbone_in.fasta
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 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) : yes
Temporary result files:
Saved as CAF (otc) : yes
Saved as CAF (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 : Lu000z_out.caf
MAF : Lu000z_out.maf
FASTA : Lu000z_out.unpadded.fasta
FASTA quality : Lu000z_out.unpadded.fasta.qual
FASTA (padded) : Lu000z_out.padded.fasta
FASTA qual.(pad): Lu000z_out.padded.fasta.qual
GAP4 (directory): Lu000z_out.gap4da
ACE : Lu000z_out.ace
HTML : Lu000z_out.html
Simple text : Lu000z_out.txt
TCS overview : Lu000z_out.tcs
Wiggle : Lu000z_out.wig
------------------------------------------------------------------------------
Creating directory Lu000z_assembly ... done.
Creating directory Lu000z_assembly/Lu000z_d_log ... done.
Creating directory Lu000z_assembly/Lu000z_d_results ... done.
Creating directory Lu000z_assembly/Lu000z_d_info ... done.
Creating directory Lu000z_assembly/Lu000z_d_chkpt ... done.
Localtime: Tue Mar 30 14:09:47 2010
Loading data (Solexa) from FASTQ files,
Fatal Error (may be due to problems of the input data):
"Could not open FASTQ file 'Lu000z_in.solexa.fastq'. Is it present? Is it
readable? Did you want to load your data in another format?"
->Thrown: void ReadPool::loadDataFromFASTQ(const string & filename, const
string & qualfilename, const bool generatefilenames, const uint8 seqtype, const
uint8 loadaction)
->Caught: Assembly::loadFASTQ(const string & fastqfile, const string &
fastaqualfile, const uint8 seqtype, const uint8 loadaction)
Program aborted, 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: /home/tbanks/Downloads/mira/bin
Aborted
tbanks@mbwinnr502727:~/Downloads/mira/bin$
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