Hi,When I run runme.sh in the folder estdemo2, there is a problem at step2 and then step3.
Fatal Error (may be due to problems of the input data): "You did not specify any input sequences to be loaded." see below the complete log file: I saw that somebody else had this problem but I do not find the answer. cheers, Didier
This is miraEST V3.0.5 (production version) for EST SNP analysis in strains.Please cite: Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J., Mueller, W. E., Wetter, T. and Suhai, S. (2004), Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome Research, 14(6). Mail general questions to the MIRA talk mailing list: mira_talk@xxxxxxxxxxxxx To (un-)subsubcribe the MIRA mailing lists, see: http://www.chevreux.org/mira_mailinglists.htmlTo 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 Apr 18 18:51:03 CEST 2010On: Linux varcadia32 2.6.27-11-generic #1 SMP Thu Jan 29 19:24:39 UTC 2009 i686 GNU/LinuxCompiled 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: 8Current system: Linux tmp-casane 2.6.24-28-generic #1 SMP Fri Jun 18 12:02:15 UTC 2010 i686 GNU/LinuxParsing parameters: --job=denovo,normal,sanger,esps2 Parameters parsed without error, perfect. Starting step 2: assembling each strain for itself ------------------------------------------------------------------------------ Parameter settings seen for: Sanger data (also common parameters) Used parameter settings: General (-GE): Project name in (proin) : mira Project name out (proout) : step2 Number of threads (not) : 2 Automatic memory management (amm) : yes Keep percent memory free (kpmf) : 15 Max. process size (mps) : 0 Keep contigs in memory (kcim) : yes EST SNP pipeline step (esps) : 2 Use template information (uti) : yes Template insert size minimum (tismin): -1 Template insert size maximum (tismax): -1 Colour reads by hash frequency (crhf) : no Load reads options (-LR): Load sequence data (lsd) : no File type (ft) : caf 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) : 0 Wants quality file (wqf) : yesRead naming scheme (rns) : [san] Sanger Institute (sanger)Merge with XML trace info (mxti) : no Filecheck only (fo) : no Assembly options (-AS): Number of passes (nop) : 3 Skim each pass (sep) : yes Maximum number of RMB break loops (rbl) : 7 Minimum read length (mrl) : 80 Base default quality (bdq) : 10 Enforce presence of qualities (epoq) : yes Automatic repeat detection (ard) : no Coverage threshold (ardct) : 2 Minimum length (ardml) : 400 Grace length (ardgl) : 40 Use uniform read distribution (urd) : no Start in pass (urdsip) : 3 Cutoff multiplier (urdcm) : 1.5 Keep long repeats separated (klrs) : no 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) : 3600 Strain and backbone options (-SB): Load straindata (lsd) : yes 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) : 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) : no Read extension window length (rewl) : 30 Read extension w. maxerrors (rewme) : 2 First extension in pass (feip) : 0 Last extension in pass (leip) : 0 Clipping options (-CL): Merge with SSAHA vector screen (msvs) : no Gap size (msvsgs) : 10 Max front gap (msvsmfg) : 60 Max end gap (msvsmeg) : 120 Strict front clip (msvssfc) : 0 Strict end clip (msvssec) : 0 Possible vector leftover clip (pvlc) : no maximum len allowed (pvcmla) : 18 Quality clip (qc) : no Minimum quality (qcmq) : 20 Window length (qcwl) : 30 Bad stretch quality clip (bsqc) : no Minimum quality (bsqcmq) : 20 Window length (bsqcwl) : 30 Masked bases clip (mbc) : no Gap size (mbcgs) : 20 Max front gap (mbcmfg) : 40 Max end gap (mbcmeg) : 60 Lower case clip (lcc) : no Clip poly A/T at ends (cpat) : no Keep poly-a signal (cpkps) : no Minimum signal length (cpmsl) : 12 Max errors allowed (cpmea) : 1 Max gap from ends (cpmgfe) : 20000 Ensure minimum left clip (emlc) : no Minimum left clip req. (mlcr) : 25 Set minimum left clip to (smlc) : 30 Ensure minimum right clip (emrc) : no Minimum right clip req. (mrcr) : 10 Set minimum right clip to (smrc) : 20 Apply SKIM chimera detection clip (ascdc) : no Apply SKIM junk detection clip (asjdc) : no Propose end clips (pec) : no Bases per hash (pecbph) : 17 Parameters for SKIM algorithm (-SK): Number of threads (not) : 2 Bases per hash (bph) : 17 Hash save stepping (hss) : 4 Percent required (pr) : 70 Max hits per read (mhpr) : 30 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) : no Nasty repeat ratio (nrr) : 100 Max hashes in memory (mhim) : 15000000 MemCap: hit reduction (mchr) : 2048 Pathfinder options (-PF): Use quick rule (uqr) : yes Quick rule min len 1 (qrml1) : 200 Quick rule min sim 1 (qrms1) : 90 Quick rule min len 2 (qrml2) : 100 Quick rule min sim 2 (qrms2) : 95 Backbone quick overlap min len (bqoml) : 150 Align parameters for Smith-Waterman align (-AL): Bandwidth in percent (bip) : 15 Bandwidth max (bmax) : 100 Bandwidth min (bmin) : 25 Minimum score (ms) : 30 Minimum overlap (mo) : 30 Minimum relative score in % (mrs) : 75 Solexa_hack_max_errors (shme) : 0 Extra gap penalty (egp) : yes extra gap penalty level (egpl) : [san] reject_codongaps Max. egp in percent (megpp) : 100 Contig parameters (-CO): Name prefix (np) : step2 Reject on drop in relative alignment score in % (rodirs) : 10 Mark repeats (mr) : yes Only in result (mroir) : no Assume SNP instead of repeats (asir) : no Minimum reads per group needed for tagging (mrpg) : 2 Minimum neighbour quality needed for tagging (mnq) : 20 Minimum Group Quality needed for RMB Tagging (mgqrt) : 30 End-read Marking Exclusion Area in bases (emea) : 15 Also mark gap bases (amgb) : yes Also mark gap bases - even multicolumn (amgbemc) : yes Also mark gap bases - need both strands (amgbnbs): yes Force non-IUPAC consensus per sequencing type (fnicpst) : yes Merge short reads (msr) : no Gap override ratio (gor) : 66 Edit options (-ED): Automatic contig editing (ace) : 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 : step2_assembly For writing result files : step2_assembly/step2_d_results For writing result info files : step2_assembly/step2_d_info For writing log files : step2_assembly/step2_d_log For writing checkpoint files : step2_assembly/step2_d_chkpt File names (-FN): When loading sequences from FASTA : mira_in.sanger.fastaWhen loading qualities from FASTA quality : mira_in.sanger.fasta.qualWhen loading sequences from FASTQ : mira_in.sanger.fastq When loading project from CAF : mira_in.sanger.caf When loading project from MAF (disabled) : mira_in.sanger.maf When loading EXP fofn : mira_in.sanger.fofn When loading project from PHD : mira_in.phd.1 When loading strain data : mira_straindata_in.txtWhen loading XML trace info files : mira_traceinfo_in.sanger.xml When loading SSAHA vector screen results : mira_ssaha2vectorscreen_in.txtWhen loading backbone from MAF : mira_backbone_in.maf When loading backbone from CAF : mira_backbone_in.caf When loading backbone from GenBank : mira_backbone_in.gbf When loading backbone from FASTA : mira_backbone_in.fasta Output files (-OUTPUT/-OUT): Save simple singlets in project (sssip) : no Save tagged singlets in project (stsip) : 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) : 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) : 60TEXT end gap fill character (tegfc) : HTML end gap fill character (hegfc) :File / directory output names: CAF : step2_out.caf MAF : step2_out.maf FASTA : step2_out.unpadded.fasta FASTA quality : step2_out.unpadded.fasta.qual FASTA (padded) : step2_out.padded.fasta FASTA qual.(pad): step2_out.padded.fasta.qual GAP4 (directory): step2_out.gap4da ACE : step2_out.ace HTML : step2_out.html Simple text : step2_out.txt TCS overview : step2_out.tcs Wiggle : step2_out.wig ------------------------------------------------------------------------------ Assembly of strain step1_snpsinSTRAIN_jerry.caf(jerry) Creating directory step2_jerry_assembly ... done. Creating directory step2_jerry_assembly/step2_jerry_d_log ... done. Creating directory step2_jerry_assembly/step2_jerry_d_results ... done. Creating directory step2_jerry_assembly/step2_jerry_d_info ... done. Creating directory step2_jerry_assembly/step2_jerry_d_chkpt ... done. Localtime: Tue Jul 27 16:36:15 2010========================== Memory self assessment ==============================Running in 32 bit mode. Dump from /proc/meminfo -------------------------------------------------------------------------------- MemTotal: 3360124 kB MemFree: 793544 kB Buffers: 645544 kB Cached: 1404800 kB SwapCached: 0 kB Active: 665304 kB Inactive: 1663332 kB HighTotal: 2480448 kB HighFree: 784004 kB LowTotal: 879676 kB LowFree: 9540 kB SwapTotal: 9839772 kB SwapFree: 9839772 kB Dirty: 480 kB Writeback: 0 kB AnonPages: 278136 kB Mapped: 106600 kB Slab: 94648 kB SReclaimable: 74308 kB SUnreclaim: 20340 kB PageTables: 3036 kB NFS_Unstable: 0 kB Bounce: 0 kB CommitLimit: 11519832 kB Committed_AS: 1050976 kB VmallocTotal: 114680 kB VmallocUsed: 11496 kB VmallocChunk: 102516 kB -------------------------------------------------------------------------------- Dump from /proc/self/status -------------------------------------------------------------------------------- Name: miraSearchESTSN State: R (running) Tgid: 20695 Pid: 20695 PPid: 20607 TracerPid: 0 Uid: 1000 1000 1000 1000 Gid: 1000 1000 1000 1000 FDSize: 32 Groups: 4 20 24 25 29 30 44 46 107 109 115 1000 VmPeak: 4520 kB VmSize: 4516 kB VmLck: 0 kB VmHWM: 1536 kB VmRSS: 1536 kB VmData: 312 kB VmStk: 84 kB VmExe: 4096 kB VmLib: 0 kB VmPTE: 16 kB Threads: 1 SigQ: 0/32768 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000000000000 SigCgt: 0000000180000000 CapInh: 0000000000000000 CapPrm: 0000000000000000 CapEff: 0000000000000000 Cpus_allowed: 03 Mems_allowed: 1 voluntary_ctxt_switches: 6 nonvoluntary_ctxt_switches: 6 -------------------------------------------------------------------------------- Information on current assembly object: AS_readpool: 0 reads. AS_contigs: 0 contigs. AS_bbcontigs: 0 contigs. Mem used for reads: 60 (60 B) Memory used in assembly structures:Eff. Size Free cap. LostByAlign AS_writtenskimhitsperid: 0 12 B 0 B 0 B AS_skim_edges: 0 12 B 0 B 0 B AS_adsfacts: 0 12 B 0 B 0 B AS_confirmed_edges: 0 12 B 0 B 0 B AS_permanent_overlap_bans: 0 12 B 0 B 0 B AS_readhitmiss: 0 12 B 0 B 0 B AS_readhmcovered: 0 12 B 0 B 0 B AS_count_rhm: 0 12 B 0 B 0 B AS_clipleft: 0 12 B 0 B 0 B AS_clipright: 0 12 B 0 B 0 B AS_used_ids: 0 12 B 0 B 0 B AS_multicopies: 0 12 B 0 B 0 B AS_hasmcoverlaps: 0 12 B 0 B 0 B AS_maxcoveragereached: 0 12 B 0 B 0 B AS_coverageperseqtype: 0 12 B 0 B 0 B AS_istroublemaker: 0 12 B 0 B 0 B AS_isdebris: 0 12 B 0 B 0 B AS_needalloverlaps: 0 20 B 0 B 0 B AS_readsforrepeatresolve: 0 20 B 0 B 0 B AS_allrmbsok: 0 12 B 0 B 0 B AS_probablermbsnotok: 0 12 B 0 B 0 B AS_weakrmbsnotok: 0 12 B 0 B 0 B AS_readmaytakeskim: 0 20 B 0 B 0 B AS_skimstaken: 0 20 B 0 B 0 B AS_numskimoverlaps: 0 12 B 0 B 0 B AS_numleftextendskims: 0 12 B 0 B 0 B AS_rightextendskims: 0 12 B 0 B 0 B AS_skimleftextendratio: 0 12 B 0 B 0 B AS_skimrightextendratio: 0 12 B 0 B 0 B AS_usedlogfiles: 0 8 B 0 B 0 BTotal: 448 (448 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: mainAborting 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. CWD: /home/casane/mira32/minidemo/estdemo2 Thank you for noticing that this is *NOT* a crash, but a controlled program stop.
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