[mira_talk] mira assembly error
- From: "Chauhan, Archana" <achauha1@xxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 24 Apr 2012 19:25:04 +0000
Hi,
I am trying to assemble my 454 upaired and the paired reads. I used the
following command to direct the output to a directory "$TMPDIR". This
directory is guaranteed to use a local hard drive.
"mira --project=HK44 --job=denovo,genome,accurate,454, -DI:$TMPDIR
>&log_assembly"
and got the following error:
Creating directory HK44_assembly ... done.
Creating directory /6621804.1.medium_chi ...
Fatal error (may be due to problems of the input data or parameters):
"Could not make sure that a needed directory exists, aborting MIRA."
->Thrown: void Assembly::ensureStandardDirectories(bool purge)
->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.
I double checked with our administrator to make sure that the directory is not
on the NFS mount.
I than ran the following command (not recomended) to make mira run:
"mira --project=HK44 --job=denovo,genome,accurate,454, -MI:sonfs=no
>&log_assembly"
And I got the following error:
WARNING WARNING WARNING!
It looks like the tmp directory is on a NFS (Network File System) 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:trt to redirect the tmp 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=no" to tell MIRA not
to stop when it finds the tmp directory on NFS.
If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.
Localtime: Tue Apr 24 13:50:39 2012
Loading data (454) from FASTQ files,
Localtime: Tue Apr 24 13:50:39 2012
Fatal error (may be due to problems of the input data or parameters):
"Could not open FASTQ file 'HK44_in.454.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)
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.
My data files look ok . Below is the snapshots of my qual and fasta files:
[cid:image003.jpg@01CD222E.60A1AA20]
[cid:image004.jpg@01CD222E.60A1AA20]
Also attached please find the log files. Can someone help me. I want mira to
work because I have to do hybrid assembly using 454, illumina n sanger reads.
Thanks,
Arc
This is MIRA V3.4.0 (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.
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
Sun Aug 21 17:50:30 CEST 2011
On: Linux arcadia 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC 2011
x86_64 x86_64 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: sh: module: line 1: syntax error: unexpected end of file
sh: error importing function definition for `module'
Linux chi29 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:09:22 EDT 2010 x86_64
x86_64 x86_64 GNU/Linux
Parsing parameters: --project=HK44 --job=denovo,genome,accurate,454,
-DI:/tmp/6621804.1.medium_chi
/
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) : HK44
Project name out (proout) : HK44
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] 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
[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] 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] 0
[454] 0
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) : HK44
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 : HK44_assembly
For writing result files : HK44_assembly/HK44_d_results
For writing result info files : HK44_assembly/HK44_d_info
For writing tmp files : /6621804.1.medium_chi
Tmp redirected to (trt) :
For writing checkpoint files : HK44_assembly/HK44_d_chkpt
File names (-FN):
When loading sequences from FASTA : [san]
HK44_in.sanger.fasta
[454] HK44_in.454.fasta
When loading qualities from FASTA quality : [san]
HK44_in.sanger.fasta.qual
[454]
HK44_in.454.fasta.qual
When loading sequensh: module: line 1: syntax error: unexpected end of
file
sh: error importing function definition for `module'
sh: module: line 1: syntax error: unexpected end of file
sh: error importing function definition for `module'
mkdir: cannot create directory `/6621804.1.medium_chi': Read-only file system
Could not create directory '/6621804.1.medium_chi'.: No such file or directory
ces from FASTQ : [san] HK44_in.sanger.fastq
[454] HK44_in.454.fastq
When loading project from CAF : HK44_in.sanger.caf
When loading project from MAF (disabled) : HK44_in.sanger.maf
When loading EXP fofn : HK44_in.sanger.fofn
When loading project from PHD : HK44_in.phd.1
When loading strain data : HK44_straindata_in.txt
When loading XML trace info files : [san]
HK44_traceinfo_in.sanger.xml
[454]
HK44_traceinfo_in.454.xml
When loading SSAHA2 vector screen results :
HK44_ssaha2vectorscreen_in.txt
When loading SMALT vector screen results :
HK44_smaltvectorscreen_in.txt
When loading backbone from MAF : HK44_backbone_in.maf
When loading backbone from CAF : HK44_backbone_in.caf
When loading backbone from GenBank : HK44_backbone_in.gbf
When loading backbone from GFF3 : HK44_backbone_in.gff3
When loading backbone from FASTA : HK44_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 : HK44_out.caf
MAF : HK44_out.maf
FASTA : HK44_out.unpadded.fasta
FASTA quality : HK44_out.unpadded.fasta.qual
FASTA (padded) : HK44_out.padded.fasta
FASTA qual.(pad): HK44_out.padded.fasta.qual
GAP4 (directory): HK44_out.gap4da
ACE : HK44_out.ace
HTML : HK44_out.html
Simple text : HK44_out.txt
TCS overview : HK44_out.tcs
Wiggle : HK44_out.wig
------------------------------------------------------------------------------
Creating directory HK44_assembly ... done.
Creating directory /6621804.1.medium_chi ...
Fatal error (may be due to problems of the input data or parameters):
"Could not make sure that a needed directory exists, aborting MIRA."
->Thrown: void Assembly::ensureStandardDirectories(bool purge)
->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.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /data/achauha1/grid/assembly/arc_042312
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Other related posts:
