[mira_talk] problem in denovo assembly fasta file
- From: Amit Bikram <amitbikram87@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 18 Nov 2013 16:45:09 +0530
Hi.
i have used this command
mira --project=isab --job=denovo,genome,accurate,454
--fasta=isab_in.454.fa 454_SETTINGS -LR:wqf=no > log.txt
and i am getting this error
This is MIRA V3.4.1.1 (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.
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
Wed Nov 14 23:07:20 CET 2012
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 orf-desktop 3.8.0-32-generic #47-Ubuntu SMP Tue Oct 1
22:35:23 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=isab --job=denovo,genome,accurate,454
--fasta=isab_in.454.fa 454_SETTINGS -LR:wqf=no
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), 454 data
Used parameter settings:
General (-GE):
Project name in (proin) : isab
Project name out (proout) : isab
Number of threads (not) : 2
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
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) : yes
Load reads options (-LR):
Load sequence data (lsd) : [san] no
[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] no
Read naming scheme (rns) : [san] Sanger Institute
(sanger)
[454] forward/reverse
(fr)
Merge with XML trace info (mxti) : [san] no
[454] yes
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
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [san] 80
[454] 40
Minimum reads per contig (mrpc) : [san] 2
[454] 5
Base default quality (bdq) : [san] 10
[454] 10
Enforce presence of qualities (epoq) : [san] yes
[454] yes
Automatic repeat detection (ard) : yes
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) : 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):
Load straindata (lsd) : no
Assign default strain (ads) : [san] no
[454] no
Default strain name (dsn) : [san] StrainX
[454] StrainX
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) : ReferenceStrain
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] yes
[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 SSAHA2/SMALT 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] yes
[454] no
maximum len allowed (pvcmla) : [san] 18
[454] 18
Min qual. threshold for entire read (mqtfer): [san] 0
[454] 0
Number of bases (mqtfernob) : [san] 0
[454] 0
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] yes
[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] no
[454] no
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] 9
[454] 9
Clip 3 prime polybase (c3pp) : [san] no
[454] no
Minimum signal length (c3ppmsl) : [san] 12
[454] 12
Max errors allowed (c3ppmea) : [san] 2
[454] 2
Max gap from ends (c3ppmgfe) : [san] 9
[454] 9
Clip known adaptors right (ckar) : [san] no
[454] yes
Ensure minimum left clip (emlc) : [san] yes
[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) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : yes
Bases per hash (pecbph) : 27
Handle Solexa GGCxG problem (pechsgp) : yes
Clip bad solexa ends (cbse) : 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) : 2000
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : no
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
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
Max. start cache fill time (mscft) : 5
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] 17
[454] 20
Minimum relative score in % (mrs) : [san] 70
[454] 70
Solexa_hack_max_errors (shme) : [san] -1
[454] -1
Extra gap penalty (egp) : [san] no
[454] yes
extra gap penalty level (egpl) : [san] low
[454] reject_codongaps
Max. egp in percent (megpp) : [san] 100
[454] 100
Contig parameters (-CO):
Name prefix (np) : isab
Reject on drop in relative alignment score in % (rodirs) : [san] 25
[454] 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
[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] 1
[454] 1
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
Keep ends unmerged (msrkeu) : [san] -1
[454] -1
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
Extended log (el) : no
Large contig size (lcs) : 500
Large contig size for stats(lcs4s) : 5000
Stop on max read name length (somrnl) : 40
Directories (-DI):
Working directory :
When loading EXP files :
When loading SCF files :
Top directory for writing files : isab_assembly
For writing result files : isab_assembly/isab_d_results
For writing result info files : isab_assembly/isab_d_info
For writing tmp files : isab_assembly/isab_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files : isab_assembly/isab_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san] isab_in.454.fa
[454] isab_in.454.fa
When loading qualities from FASTA quality : [san]
isab_in.454.fa.qual
[454]
isab_in.454.fa.qual
When loading sequences from FASTQ : [san]
isab_in.sanger.fastq
[454] isab_in.454.fastq
When loading project from CAF : isab_in.sanger.caf
When loading project from MAF (disabled) : isab_in.sanger.maf
When loading EXP fofn : isab_in.sanger.fofn
When loading project from PHD : isab_in.phd.1
When loading strain data : isab_straindata_in.txt
When loading XML trace info files : [san]
isab_traceinfo_in.sanger.xml
[454]
isab_traceinfo_in.454.xml
When loading SSAHA2 vector screen results :
isab_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
isab_smaltvectorscreen_in.txt
When loading backbone from MAF : isab_backbone_in.maf
When loading backbone from CAF : isab_backbone_in.caf
When loading backbone from GenBank : isab_backbone_in.gbf
When loading backbone from GFF3 : isab_backbone_in.gff3
When loading backbone from FASTA : isab_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 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) : yes
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 : isab_out.caf
MAF : isab_out.maf
FASTA : isab_out.unpadded.fasta
FASTA quality : isab_out.unpadded.fasta.qual
FASTA (padded) : isab_out.padded.fasta
FASTA qual.(pad): isab_out.padded.fasta.qual
GAP4 (directory): isab_out.gap4da
ACE : isab_out.ace
HTML : isab_out.html
Simple text : isab_out.txt
TCS overview : isab_out.tcs
Wiggle : isab_out.wig
------------------------------------------------------------------------------
Creating directory isab_assembly ... done.
Creating directory isab_assembly/isab_d_tmp ... done.
Creating directory isab_assembly/isab_d_results ... done.
Creating directory isab_assembly/isab_d_info ... done.
Creating directory isab_assembly/isab_d_chkpt ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Mon Nov 18 14:30:46 2013
Loading data (454) from FASTA files,
Could not find FASTA quality file isab_in.454.fa.qual, using default values
for these reads.
Localtime: Mon Nov 18 14:30:46 2013
Counting sequences in FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
Found 4758954 sequences.
Localtime: Mon Nov 18 14:31:15 2013
454 will load 4758954 reads.
Longest Sanger: 0
Longest 454: 1196
Longest IonTor: 0
Longest PacBio: 0
Longest Solexa: 0
Longest Solid: 0
Longest overall: 1196
Total reads to load: 4758954
Reserving space for reads (this may take a while)
Reserved space for 4758964 reads.
Loading data (454) from FASTA files,
Could not find FASTA quality file isab_in.454.fa.qual, using default values
for these reads.
Localtime: Mon Nov 18 14:31:15 2013
Localtime: Mon Nov 18 14:31:15 2013
Loading data from FASTA file:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|...
this is in log file and in command line it shows KILLED
please help me to find out the error
with regards
Amit
Other related posts:
