[mira_talk] Re: FW: 454 assembly
- From: "Shabhonam Caim (TGAC)" <Shabhonam.Caim@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 Jul 2010 10:36:37 +0100
Thanks thomas for your reply but still I am getting error:
I have used the following command and provided the qual file as well :
mira --project=test --job=denovo,genome,draft 454_SETTINGS
-FN:fai=2.GAC.454Reads.fna -FN:fqui=2.GAC.454Reads.qual
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
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
Directories (-DI):
When loading EXP files :
When loading SCF files :
Top directory for writing files : test_assembly
For writing result files : test_assembly/test_d_results
For writing result info files : test_assembly/test_d_info
For writing log files : test_assembly/test_d_log
For writing checkpoint files : test_assembly/test_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
test_in.sanger.fasta
[454]
2.GAC.454Reads.fna
When loading qualities from FASTA quality : [san]
test_in.sanger.fasta.qual
[454]
2.GAC.454Reads.qual
When loading sequences from FASTQ : [san]
test_in.sanger.fastq
[454] test_in.454.fastq
When loading project from CAF : test_in.sanger.caf
When loading project from MAF (disabled) : test_in.sanger.maf
When loading EXP fofn : test_in.fofn
When loading project from PHD : test_in.phd.1
When loading strain data : test_straindata_in.txt
When loading XML trace info files : [san]
test_traceinfo_in.sanger.xml
[454]
test_traceinfo_in.454.xml
When loading SSAHA vector screen results :
test_ssaha2vectorscreen_in.txt
When loading backbone from MAF : test_backbone_in.maf
When loading backbone from CAF : test_backbone_in.caf
When loading backbone from GenBank : test_backbone_in.gbf
When loading backbone from FASTA : test_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) : 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 : test_out.caf
MAF : test_out.maf
FASTA : test_out.unpadded.fasta
FASTA quality : test_out.unpadded.fasta.qual
FASTA (padded) : test_out.padded.fasta
FASTA qual.(pad): test_out.padded.fasta.qual
GAP4 (directory): test_out.gap4da
ACE : test_out.ace
HTML : test_out.html
Simple text : test_out.txt
TCS overview : test_out.tcs
Wiggle : test_out.wig
------------------------------------------------------------------------------
Deleting old directory test_assembly ... done.
Creating directory test_assembly ... done.
Creating directory test_assembly/test_d_log ... done.
Creating directory test_assembly/test_d_results ... done.
Creating directory test_assembly/test_d_info ... done.
Creating directory test_assembly/test_d_chkpt ... done.
Localtime: Thu Jul 22 10:31:49 2010
========================== Memory self assessment ==============================
Running in 64 bit mode.
Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal: 8174224 kB
MemFree: 94968 kB
Buffers: 4644 kB
Cached: 4976444 kB
SwapCached: 287504 kB
Active: 6618732 kB
Inactive: 1307228 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 8174224 kB
LowFree: 94968 kB
SwapTotal: 2031608 kB
SwapFree: 1476740 kB
Dirty: 1984 kB
Writeback: 0 kB
AnonPages: 2936468 kB
Mapped: 32408 kB
Slab: 81840 kB
PageTables: 37252 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 6118720 kB
Committed_AS: 5290616 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 263728 kB
VmallocChunk: 34359474579 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
--------------------------------------------------------------------------------
Dump from /proc/self/status
--------------------------------------------------------------------------------
Name: mira
State: R (running)
SleepAVG: 0%
Tgid: 6158
Pid: 6158
PPid: 17617
TracerPid: 0
Uid: 8395 8395 8395 8395
Gid: 3658 3658 3658 3658
FDSize: 256
Groups: 3658
VmPeak: 4972 kB
VmSize: 4920 kB
VmLck: 0 kB
VmHWM: 1744 kB
VmRSS: 1744 kB
VmData: 464 kB
VmStk: 84 kB
VmExe: 4336 kB
VmLib: 0 kB
VmPTE: 28 kB
StaBrk: 00a7e000 kB
Brk: 017f0000 kB
StaStk: 7fffc798fa70 kB
Threads: 1
SigQ: 0/71680
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
Cpus_allowed:
00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
Mems_allowed: 00000000,00000001
--------------------------------------------------------------------------------
Information on current assembly object:
AS_readpool: 0 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 112 (112 B)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 0 24 B 0 B 0 B
AS_skim_edges: 0 24 B 0 B 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: 0 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: 0 24 B 0 B 0 B
AS_clipright: 0 24 B 0 B 0 B
AS_used_ids: 0 24 B 0 B 0 B
AS_multicopies: 0 24 B 0 B 0 B
AS_hasmcoverlaps: 0 24 B 0 B 0 B
AS_maxcoveragereached: 0 24 B 0 B 0 B
AS_coverageperseqtype: 0 24 B 0 B 0 B
AS_istroublemaker: 0 24 B 0 B 0 B
AS_isdebris: 0 24 B 0 B 0 B
AS_needalloverlaps: 0 40 B 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_usedlogfiles: 1 48 B 0 B 0 B
Total: 920 (920 B)
================================================================================
Dynamic allocs: 0
Align allocs: 0
Fatal Error (may be due to problems of the input data):
"You did not specify any input sequences to be loaded."
->Thrown: void Assembly::loadSequenceData_new()
->Caught: main
Cheers
Shab
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Thomas Müller
Sent: 22 July 2010 10:12
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: FW: 454 assembly
try:
mira --project=test --job=denovo,genome,draft,est 454_SETTINGS
-FN:fai=2.GAC.454Reads.fna
But you should really also add the .qual file with FN:fqui=2.GAC.454Reads.qual
cheers
Thomas
On Jul 22, 2010, at 10:53 AM, Shabhonam Caim (TGAC) wrote:
Hello Mira Users
I am trying to assemble the 454 reads using Mira by using following command:
mira-3.0.0 mira --project=test --job=denovo,genome,draft,2.GAC.454Reads.fna
and I am getting the following error:
This is MIRA V3.0.0 (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.
Mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx<mailto:mira_talk@xxxxxxxxxxxxx>
To (un-)subsubcribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
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
Sun Jan 31 20:23:36 CET 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 n57140 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008
x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=454asembly --job=denovo, genome, draft
pk.454.fasta
Seen no assembly quality in job definition, assuming 'normal'.
Seen no assembly type in job definition, assuming 'genome'.
,..
========================= Parameter parsing error(s) ==========================
* Parameter section: '(none)'
* unrecognised string or unexpected character: genome
* Parameter section: '(none)'
* unrecognised string or unexpected character: draft
* Parameter section: '(none)'
* unrecognised string or unexpected character: pk
* Parameter section: '(none)'
* unrecognised string or unexpected character: 454
* Parameter section: '(none)'
* unrecognised string or unexpected character: fasta
===============================================================================
Fatal Error (may be due to problems of the input data):
"Error while parsing parameters, sorry."
->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> & Pv,
MIRAParameters * singlemp)
->Caught: main
Or can I please get the commands to run the 454 assembly (basic denovo assembly
with default parameters)
cheers
Shab
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