Dear sir,
I successfully installed and do a run in mira. I got this error...:hereby i
attached my manifest also. my data was the illumina RNA-seq data. The species
is Drosophila.Could you give me some suggestion?Thanks & Regards,Zan Zhang
EORROR:This is MIRA 4.0.2 .
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
Fri Apr 18 14:57:20 CEST 2014
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 node7 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36
EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
Looking for files named in data ...Pushing back filename:
"/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_1.fastq.cleaned.renamed.fastq"
Pushing back filename:
"/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_2.fastq.cleaned.renamed.fastq"
Manifest:
projectname: MyFirstAssembly
job: est,denovo,accurate
parameters: COMMON_SETTINGS -GE:not=1 amm=off -HS:mnr=yes:nrr=8
Manifest load entries: 1
MLE 1:
RGID: 1
RGN: DataIlluminaPairedLib SN: StrainX
SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
ST: 6 (Solexa) namschem: 4 SID: 0
DQ: 30
BB: 0 Rail: 0 CER: 0
/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_1.fastq.cleaned.renamed.fastq
/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_2.fastq.cleaned.renamed.fastq
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data
Used parameter settings:
General (-GE):
Project name : MyFirstAssembly
Number of threads (not) : 1
Automatic memory management (amm) : no
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Colour reads by hash frequency (crhf) : no
Load reads options (-LR):
Wants quality file (wqf) : [sxa] yes
Filecheck only (fo) : no
Assembly options (-AS):
Number of passes (nop) : 4
Skim each pass (sep) : yes
Maximum number of RMB break loops (rbl) : 2
Maximum contigs per pass (mcpp) : 0
Minimum read length (mrl) : [sxa] 20
Minimum reads per contig (mrpc) : [sxa] 4
Enforce presence of qualities (epoq) : [sxa] yes
Automatic repeat detection (ard) : no
Coverage threshold (ardct) : [sxa] 2.5
Minimum length (ardml) : [sxa] 300
Grace length (ardgl) : [sxa] 20
Use uniform read distribution (urd) : no
Start in pass (urdsip) : 3
Cutoff multiplier (urdcm) : [sxa] 1.5
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) : 360
Strain and backbone options (-SB):
Bootstrap new backbone (bnb) : yes
Start backbone usage in pass (sbuip) : 3
Backbone rail from strain (brfs) :
Backbone rail length (brl) : 0
Backbone rail overlap (bro) : 0
Trim overhanging reads (tor) : yes
(Also build new contigs (abnc)) : yes
Dataprocessing options (-DP):
Use read extensions (ure) : [sxa] no
Read extension window length (rewl) : [sxa] 30
Read extension w. maxerrors (rewme) : [sxa] 2
First extension in pass (feip) : [sxa] 0
Last extension in pass (leip) : [sxa] 0
Clipping options (-CL):
SSAHA2 or SMALT clipping:
Gap size (msvsgs) : [sxa] 1
Max front gap (msvsmfg) : [sxa] 2
Max end gap (msvsmeg) : [sxa] 2
Strict front clip (msvssfc) : [sxa] 0
Strict end clip (msvssec) : [sxa] 0
Possible vector leftover clip (pvlc) : [sxa] no
maximum len allowed (pvcmla) : [sxa] 18
Min qual. threshold for entire read (mqtfer): [sxa] 5
Number of bases (mqtfernob) : [sxa] 15
Quality clip (qc) : [sxa] no
Minimum quality (qcmq) : [sxa] 20
Window length (qcwl) : [sxa] 30
Bad stretch quality clip (bsqc) : [sxa] no
Minimum quality (bsqcmq) : [sxa] 5
Window length (bsqcwl) : [sxa] 20
Masked bases clip (mbc) : [sxa] yes
Gap size (mbcgs) : [sxa] 5
Max front gap (mbcmfg) : [sxa] 12
Max end gap (mbcmeg) : [sxa] 12
Lower case clip front (lccf) : [sxa] no
Lower case clip back (lccb) : [sxa] no
Clip poly A/T at ends (cpat) : [sxa] yes
Keep poly-a signal (cpkps) : [sxa] yes
Minimum signal length (cpmsl) : [sxa] 15
Max errors allowed (cpmea) : [sxa] 1
Max gap from ends (cpmgfe) : [sxa] 20000
Clip 3 prime polybase (c3pp) : [sxa] yes
Minimum signal length (c3ppmsl) : [sxa] 15
Max errors allowed (c3ppmea) : [sxa] 3
Max gap from ends (c3ppmgfe) : [sxa] 9
Clip known adaptors right (ckar) : [sxa] yes
Ensure minimum left clip (emlc) : [sxa] no
Minimum left clip req. (mlcr) : [sxa] 0
Set minimum left clip to (smlc) : [sxa] 0
Ensure minimum right clip (emrc) : [sxa] no
Minimum right clip req. (mrcr) : [sxa] 10
Set minimum right clip to (smrc) : [sxa] 20
Apply SKIM chimera detection clip (ascdc) : yes
Apply SKIM junk detection clip (asjdc) : no
Propose end clips (pec) : [sxa] yes
Bases per hash (pecbph) : 31
Handle Solexa GGCxG problem (pechsgp) : yes
Front freq (pffreq) : [sxa] 0
Back freq (pbfreq) : [sxa] 0
Minimum kmer for forward-rev (pmkfr) : 1
Front forward-rev (pffore) : [sxa] yes
Back forward-rev (pbfore) : [sxa] yes
Front conf. multi-seq type (pfcmst) : [sxa] yes
Back conf. multi-seq type (pbcmst) : [sxa] yes
Front seen at low pos (pfsalp) : [sxa] no
Back seen at low pos (pbsalp) : [sxa] no
Clip bad solexa ends (cbse) : [sxa] yes
Search PhiX174 (spx174) : [sxa] yes
Filter PhiX174 (fpx174) : [sxa] yes
Rare kmer mask (rkm) : [sxa] 2
Parameters for SKIM algorithm (-SK):
Number of threads (not) : 1
Also compute reverse complements (acrc) : yes
Bases per hash (bph) : 23
Automatic increase per pass (bphaipp) : 1 Automatic
incr. cov. threshold (bphaict): 20
Hash save stepping (hss) : 1
Percent required (pr) : [sxa] 95
Max hits per read (mhpr) : 30
Max megahub ratio (mmhr) : 0
SW check on backbones (swcob) : no
Max hashes in memory (mhim) : 15000000
MemCap: hit reduction (mchr) : 4096
Parameters for Hash Statistics (-HS):
Freq. cov. estim. min (fcem) : 30
Freq. estim. min normal (fenn) : 0.4
Freq. estim. max normal (fexn) : 1.6
Freq. estim. repeat (fer) : 1.9
Freq. estim. heavy repeat (fehr) : 8
Freq. estim. crazy (fecr) : 20
Mask nasty repeats (mnr) : yes
Nasty repeat ratio (nrr) : 8
Nasty repeat coverage (nrc) : 200
Lossless digital normalisation (ldn) : yes
Repeat level in info file (rliif) : 6
Million hashes per buffer (mhpb) : 16
Rare kmer early kill (rkek) : no
Pathfinder options (-PF):
Use quick rule (uqr) : [sxa] yes
Quick rule min len 1 (qrml1) : [sxa] -95
Quick rule min sim 1 (qrms1) : [sxa] 100
Quick rule min len 2 (qrml2) : [sxa] -85
Quick rule min sim 2 (qrms2) : [sxa] 100
Backbone quick overlap min len (bqoml) : [sxa] 20
Max. start cache fill time (mscft) : 5
Align parameters for Smith-Waterman align (-AL):
Bandwidth in percent (bip) : [sxa] 20
Bandwidth max (bmax) : [sxa] 80
Bandwidth min (bmin) : [sxa] 20
Minimum score (ms) : [sxa] 15
Minimum overlap (mo) : [sxa] 25
Minimum relative score in % (mrs) : [sxa] 90
Solexa_hack_max_errors (shme) : [sxa] -1
Extra gap penalty (egp) : [sxa] yes
extra gap penalty level (egpl) : [sxa] reject_codongaps
Max. egp in percent (megpp) : [sxa] 100 Contig parameters
(-CO):
Name prefix (np) :
MyFirstAssembly
Reject on drop in relative alignment score in % (rodirs) : [sxa] 15
Mark repeats (mr) : yes
Only in result (mroir) : no
Assume SNP instead of repeats (asir) : no
Minimum reads per group needed for tagging (mrpg) : [sxa] 4
Minimum neighbour quality needed for tagging (mnq) : [sxa] 20
Minimum Group Quality needed for RMB Tagging (mgqrt) : [sxa] 30
End-read Marking Exclusion Area in bases (emea) : [sxa] 1
Set to 1 on clipping PEC (emeas1clpec) : yes
Also mark gap bases (amgb) : [sxa] yes
Also mark gap bases - even multicolumn (amgbemc) : [sxa] yes
Also mark gap bases - need both strands (amgbnbs): [sxa] yes
Force non-IUPAC consensus per sequencing type (fnicpst) : [sxa] no
Merge short reads (msr) : [sxa] yes
Max errors (msrme) : [sxa] 0
Keep ends unmerged (msrkeu) : [sxa] -1
Gap override ratio (gor) : [sxa] 66
Edit options (-ED):
Mira automatic contig editing (mace) : yes
Edit kmer singlets (eks) : yes
Edit homopolymer overcalls (ehpo) : [sxa] no
Misc (-MI):
Large contig size (lcs) : 500
Large contig size for stats (lcs4s) : 1000
I know what I do (ikwid) : no
Extra flag 1 / sanity track check (ef1) : no
Extra flag 2 / dnredreadsatpeaks (ef2) : yes
Extra flag 3 / pelibdisassemble (ef3) : yes
Extended log (el) : no
Nag and Warn (-NW):
Check NFS (cnfs) : stop
Check multi pass mapping (cmpm) : stop
Check template problems (ctp) : stop
Check duplicate read names (cdrn) : stop
Check max read name length (cmrnl) : stop
Max read name length (mrnl) : 40
Check average coverage (cac) : stop
Average coverage value (acv) : 80
Directories (-DI):
Top directory for writing files : MyFirstAssembly_assembly
For writing result files :
MyFirstAssembly_assembly/MyFirstAssembly_d_results
For writing result info files :
MyFirstAssembly_assembly/MyFirstAssembly_d_info
For writing tmp files :
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp
Tmp redirected to (trt) :
For writing checkpoint files :
MyFirstAssembly_assembly/MyFirstAssembly_d_chkpt
Output files (-OUTPUT/-OUT):
Save simple singlets in project (sssip) : [sxa] no
Save tagged singlets in project (stsip) : [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) : 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 : MyFirstAssembly_out.caf
MAF : MyFirstAssembly_out.maf
FASTA : MyFirstAssembly_out.unpadded.fasta
FASTA quality : MyFirstAssembly_out.unpadded.fasta.qual FASTA
(padded) : MyFirstAssembly_out.padded.fasta
FASTA qual.(pad): MyFirstAssembly_out.padded.fasta.qual
GAP4 (directory): MyFirstAssembly_out.gap4da
ACE : MyFirstAssembly_out.ace
HTML : MyFirstAssembly_out.html
Simple text : MyFirstAssembly_out.txt
TCS overview : MyFirstAssembly_out.tcs
Wiggle : MyFirstAssembly_out.wig
------------------------------------------------------------------------------
Creating directory MyFirstAssembly_assembly ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_results ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_info ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_chkpt ... done.
Creating directory MyFirstAssembly_assembly/MyFirstAssembly_d_tmp ... done.
Tmp directory is not on a NFS mount, good.
Localtime: Thu Jun 12 15:42:14 2014
Loading reads from
/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_1.fastq.cleaned.renamed.fastq
type fastq
Localtime: Thu Jun 12 15:42:14 2014
Loading data from FASTQ file:
/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_1.fastq.cleaned.renamed.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 31236815 reads, Localtime: Thu Jun 12 15:52:54 2014
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Loading reads from
/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_2.fastq.cleaned.renamed.fastq
type fastq
Localtime: Thu Jun 12 15:53:17 2014
Loading data from FASTQ file:
/data-SATA/home/liuying/transcriptome/illumina/Drosophila_melanogaster/SRR927153_assemble/remove_low_quality_data/SRR927153_2.fastq.cleaned.renamed.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)
Done.
Loaded 31236815 reads, Localtime: Thu Jun 12 16:05:03 2014
Looking at FASTQ type ... guessing FASTQ-33 (Sanger)
Running quality values adaptation ... done.
Checking reads for trace data (loading qualities if needed):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%]
No SCF data present in any read, EdIt automatic contig editing for Sanger data
is now switched off.
62473630 reads with valid data for assembly.
Localtime: Thu Jun 12 16:07:07 2014
Generated 31236815 unique DNA template ids for 62473630 valid reads.
TODO: Like Readpool: strain x has y reads
Have read pool with 62473630 reads.
===========================================================================
Pool statistics:
Backbones: 0 Backbone rails: 0
Sanger 454 IonTor PcBioHQ PcBioLQ Text Solexa SOLiD
------------------------------------------------------------
Total reads 0 0 0 0 0 0 62473630 0
Reads wo qual 0 0 0 0 0 0 0 0
Used reads 0 0 0 0 0 0 62473630 0
Avg tot rlen 0 0 0 0 0 0 99 0
Avg rlen used 0 0 0 0 0 0 99 0
W/o clips 0 0 0 0 0 0 62473630 0
Solexa total bases: 6201635932 used bases in used reads: 6201635932
===========================================================================
...........................
Searching for possible overlaps:
Localtime: Sat Jun 21 14:16:56 2014
Now running threaded and partitioned skimmer with 38 partitions in 1 threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] done.
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.2.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchf_pass.2.bin
from 6901222944 to 3943452432
truncating
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.2.bin
truncated
MyFirstAssembly_assembly/MyFirstAssembly_d_tmp/MyFirstAssembly_int_posmatchc_pass.2.bin
from 6449929560 to 3850855680
Hits chosen: 649525676
Localtime: Sun Jun 22 00:49:31 2014
Total megahubs: 4948
MIRA has detected megahubs in your data.This may not be a problem, but most
probably is, especially for eukaryotes.
You have more than 0.0000000000% of your reads found to be megahubs.
You should check the following:
1) for Sanger sequences: are all the sequencing vectors masked /
clipped?
2) for 454 sequences: are all the adaptors masked / clipped?
You will find in the info directory a file called
'*_info_readrepeats.lst',
consult the MIRA manual on how to extract repeat information from there.
*ONLY* when you are sure that no (or only a very negligible number) of
sequencing
vector / adaptor sequence is remaining, try this:
3) for organisms with complex repeats (eukaryots & some bacteria):
- reduce the -HS:nrr parameter (divide by 2)
*ONLY* if the above fails, try increasing the -SK:mmhr parameter
Note that the number of present megahubs will increase computation time in
an exponential way, so be careful when changing -SK:mmhr.
You have 0.0079201417% of your reads as megahubs.
You have set a maximum allowed ratio of: 0.0000000000
Ending the assembly because the maximum ratio has been reached/surpassed.
Failure, wrapped MIRA process aborted.
Attachment:
manifest.conf
Description: Binary data
