On Thu, May 5, 2011 at 12:05 PM, Rob Good <rtgood@xxxxxxxxxxxxxx> wrote: > I have done a de novo assembly with SOAPdenovo and am now aligning it to > the reference strain with mira. > I broke all the contigs greater than 10k up but I'm getting this error and > don't know what it is referring to ... > Can someone enlighten me please??? > > > > Fatal error (may be due to problems of the input data or parameters): > *>"Read rr_####2568#### is longer than MAXREADSIZEALLOWED (29900) bases. Skim cannot handle than, sorry."* makes it seem as if there are still few contigs with size > 29900. checkout for the same and split again. Regards, Ganga Jeena > > ->Thrown: void Skim::transformSeqToVariableHash (...) > ->Caught: main > > Aborting process, probably due to error in the input data or > parametrisation. > Please check the output log for more information. > > The full log is below > > Rob Good > Ph. +61 3 8344 2347 > Mob. 0434058250 > Genetics Dept > University of Melbourne > PARKVILLE, Australia > > > This is MIRA V3.2.1 (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: bjpop > Wed Dec 8 16:18:25 EST 2010 > On: Linux bruce-m.vlsci.unimelb.edu.au 2.6.18-164.11.1.el5 #1 SMP Wed Jan > 20 07:32:21 EST 2010 x86_64 x86_64 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 bruce118 2.6.18-238.5.1.el5 #1 SMP Fri Apr 1 18:41:58 > EDT 2011 x86_64 x86_64 x86_64 GNU/Linux > > > > Parsing parameters: --project=DGRP-712 --job=genome,sanger,mapping,accurate > -SK:not=8 SANGER_SETTINGS -LR:wqf=no -AS:epoq=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) > > Used parameter settings: > General (-GE): > Project name in (proin) : DGRP-712 > Project name out (proout) : DGRP-712 > 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) : yes > Template insert size minimum (tismin) : -1 > Template insert size maximum (tismax) : -1 > Template partner build direction (tpbd) : -1 > Colour reads by hash frequency (crhf) : yes > > Load reads options (-LR): > Load sequence data (lsd) : yes > File type (ft) : 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) : 0 > > Wants quality file (wqf) : no > > Read 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) : 1 > Skim each pass (sep) : yes > Maximum number of RMB break loops (rbl) : 1 > > Minimum read length (mrl) : 80 > Minimum reads per contig (mrpc) : 2 > Base default quality (bdq) : 10 > Enforce presence of qualities (epoq) : no > > Automatic repeat detection (ard) : yes > 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) : 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) : yes > Default strain name (dsn) : StrainX > Load backbone (lb) : yes > Start backbone usage in pass (sbuip) : 0 > 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) : no > > Dataprocessing options (-DP): > Use read extensions (ure) : yes > 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 SSAHA2/SMALT 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) : yes > maximum len allowed (pvcmla) : 18 > Quality clip (qc) : no > Minimum quality (qcmq) : 20 > Window length (qcwl) : 30 > Bad stretch quality clip (bsqc) : yes > Minimum quality (bsqcmq) : 20 > Window length (bsqcwl) : 30 > Masked bases clip (mbc) : yes > 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) : 9 > Ensure minimum left clip (emlc) : yes > 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) : yes > Apply SKIM junk detection clip (asjdc) : no > > Propose end clips (pec) : yes > Bases per hash (pecbph) : 17 > Handle Solexa GGCxG problem (pechsgp) : yes > > Parameters for SKIM algorithm (-SK): > Number of threads (not) : 8 > > Also compute reverse complements (acrc) : yes > Bases per hash (bph) : 16 > Hash save stepping (hss) : 4 > Percent required (pr) : 60 > > Max hits per read (mhpr) : 1000 > 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 > 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) : 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) : 20 > Bandwidth max (bmax) : 130 > Bandwidth min (bmin) : 25 > Minimum score (ms) : 30 > Minimum overlap (mo) : 15 > Minimum relative score in % (mrs) : 65 > Solexa_hack_max_errors (shme) : 0 > Extra gap penalty (egp) : no > extra gap penalty level (egpl) : [san] low > Max. egp in percent (megpp) : 100 > > Contig parameters (-CO): > Name prefix (np) : DGRP-712 > Reject on drop in relative alignment score in % (rodirs) : 25 > 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) : 1 > Set to 1 on clipping PEC (emeas1clpec) : yes > 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) : no > Merge short reads (msr) : no > Gap override ratio (gor) : 66 > > Edit options (-ED): > Automatic contig editing (ace) : no > Sanger only: > Strict editing mode (sem) : no > Confirmation threshold in percent (ct) : 50 > > Misc (-MI): > Stop on NFS (sonfs) : yes > Large contig size (lcs) : 500 > Large contig size for stats(lcs4s) : 5000 > > Directories (-DI): > When loading EXP files : > When loading SCF files : > Top directory for writing files : DGRP-712_assembly > For writing result files : > DGRP-712_assembly/DGRP-712_d_results > For writing result info files : > DGRP-712_assembly/DGRP-712_d_info > For writing log files : DGRP-712_assembly/DGRP-712_d_log > Log redirected to (lrt) : > For writing checkpoint files : > DGRP-712_assembly/DGRP-712_d_chkpt > > File names (-FN): > When loading sequences from FASTA : > DGRP-712_in.sanger.fasta > When loading qualities from FASTA quality : > DGRP-712_in.sanger.fasta.qual > When loading sequences from FASTQ : > DGRP-712_in.sanger.fastq > When loading project from CAF : > DGRP-712_in.sanger.caf > When loading project from MAF (disabled) : > DGRP-712_in.sanger.maf > When loading EXP fofn : > DGRP-712_in.sanger.fofn > When loading project from PHD : DGRP-712_in.phd.1 > When loading strain data : > DGRP-712_straindata_in.txt > When loading XML trace info files : > DGRP-712_traceinfo_in.sanger.xml > When loading SSAHA2 vector screen results : > DGRP-712_ssaha2vectorscreen_in.txt > When loading SMALT vector screen results : > DGRP-712_smaltvectorscreen_in.txt > > When loading backbone from MAF : > DGRP-712_backbone_in.maf > When loading backbone from CAF : > DGRP-712_backbone_in.caf > When loading backbone from GenBank : > DGRP-712_backbone_in.gbf > When loading backbone from FASTA : > DGRP-712_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 MAF (orm) : 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 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 : DGRP-712_out.caf > MAF : DGRP-712_out.maf > FASTA : DGRP-712_out.unpadded.fasta > FASTA quality : DGRP-712_out.unpadded.fasta.qual > FASTA (padded) : DGRP-712_out.padded.fasta > FASTA qual.(pad): DGRP-712_out.padded.fasta.qual > GAP4 (directory): DGRP-712_out.gap4da > ACE : DGRP-712_out.ace > HTML : DGRP-712_out.html > Simple text : DGRP-712_out.txt > TCS overview : DGRP-712_out.tcs > Wiggle : DGRP-712_out.wig > > ------------------------------------------------------------------------------ > Deleting old directory DGRP-712_assembly ... done. > Creating directory DGRP-712_assembly ... done. > Creating directory DGRP-712_assembly/DGRP-712_d_log ... done. > Creating directory DGRP-712_assembly/DGRP-712_d_results ... done. > Creating directory DGRP-712_assembly/DGRP-712_d_info ... done. > Creating directory DGRP-712_assembly/DGRP-712_d_chkpt ... done. > > Log directory is not on a NFS mount, good. > > Localtime: Thu May 5 16:07:06 2011 > > Loading backbone from FASTA file: DGRP-712_backbone_in.fasta (quality: > DGRP-712_backbone_in.fasta.qual) > Localtime: Thu May 5 16:07:06 2011 > Counting sequences in FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Found 15 sequences. > Localtime: Thu May 5 16:07:10 2011 > Loading data from FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Localtime: Thu May 5 16:07:15 2011 > rnm size: 0 > Could not find FASTA quality file DGRP-712_backbone_in.fasta.qual, using > default values for these reads. > Localtime: Thu May 5 16:07:15 2011 > > Done. > Loaded 15 reads with 168736537 raw bases. > 0 reads have quality accounted for. > Postprocessing backbone(s) ... this may take a while. > 15 to process > 2L_bb 23011544 > 2LHet_bb 368872 > 2R_bb 21146708 > 2RHet_bb 3288761 > 3L_bb 24543557 > 3LHet_bb 2555491 > 3R_bb 27905053 > 3RHet_bb 2517507 > 4_bb 1351857 > M_bb 19517 > Uextra_bb 29004656 > U_bb 10049037 > X_bb 22422827 > XHet_bb 204112 > YHet_bb 347038 > Localtime: Thu May 5 16:07:24 2011 > > Seeing strain 1: "ReferenceStrain" > Generated 1 unique strain ids for 15 reads. > Strain "default" has 0 reads. > Strain "ReferenceStrain" has 15 reads. > Loading data (Sanger) from FASTA files, > Localtime: Thu May 5 16:07:24 2011 > Counting sequences in FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Found 61411 sequences. > Localtime: Thu May 5 16:07:31 2011 > Localtime: Thu May 5 16:07:31 2011 > > Checking SCF files (loading qualities only if needed): > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Done. > 0 SCF files loaded ok. > > > Sanger will load 61411 reads. > Longest Sanger: 10000 > Longest 454: 0 > Longest PacBio: 0 > Longest Solexa: 0 > Longest Solid: 0 > Longest overall: 10000 > Total reads to load: 61411 > -SB:brl is 0, automatically determining optimal value. > Optimal rail would be longer than 18k, adjusting down to 18k. > brl: 18000 > -SB:bro is 0, automatically determining optimal value. > bro: 9000 > Reserving space for reads > Reserved space for 80147 reads (including backbone rails). > Adding rails to 15 contigs (this may take a while). > Loading data (Sanger) from FASTA files, > Localtime: Thu May 5 16:09:45 2011 > Counting sequences in FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Found 61411 sequences. > Localtime: Thu May 5 16:09:48 2011 > Loading data from FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.. > Warning: C1530710_1 has no bases?! This usually points at some error in the > processing of data before it arrives to MIRA. > .. [100%] > Localtime: Thu May 5 16:09:52 2011 > rnm size: 0 > Could not find FASTA quality file DGRP-712_in.sanger.fasta.qual, using > default values for these reads. > Localtime: Thu May 5 16:09:53 2011 > > Done. > Loaded 61411 reads with 129557687 raw bases. > 0 reads have quality accounted for. > Localtime: Thu May 5 16:09:53 2011 > > Checking SCF files (loading qualities only if needed): > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Done. > 0 SCF files loaded ok. > 61410 SCF files were not found (see > 'DGRP-712_assembly/DGRP-712_d_log/DGRP-712_info_scfreadfail.0' for a list of > names). > > > Loaded 61411 Sanger reads. > Total reads loaded: 61411 > Localtime: Thu May 5 16:09:58 2011 > > Checking SCF files (loading qualities only if needed): > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Done. > 0 SCF files loaded ok. > 61410 SCF files were not found (see > 'DGRP-712_assembly/DGRP-712_d_log/DGRP-712_info_scfreadfail.0' for a list of > names). > > > Checking reads for trace data: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > No SCF data present in any read, automatic contig editing for Sanger data > is now switched off. > 80136 reads with valid data for assembly. > Localtime: Thu May 5 16:09:59 2011 > > Generated 80136 unique template ids for 80136 valid reads. > No useful template information found, template routines will not be used. > Localtime: Thu May 5 16:09:59 2011 > > Seeing strain 1: "ReferenceStrain" > Seeing strain 2: "StrainX" > Generated 2 unique strain ids for 80137 reads. > Strain "default" has 1 reads. > Strain "ReferenceStrain" has 15 reads. > Strain "StrainX" has 61410 reads. > Have read pool with 80137 reads. > C1530710_1: unable to load or other reason for invalid data. > > =========================================================================== > Pool statistics: > Backbones: 15 Backbone rails: 18711 > > Sanger 454 PacBio Solexa SOLiD > ---------------------------------------- > Total reads 61411 0 0 0 0 > Reads wo qual 61411 0 0 0 0 > Used reads 61361 0 0 0 0 > Avg tot rlen 2109 0 0 0 0 > Avg rlen used 2111 0 0 0 0 > > With strain 61411 0 0 0 0 > W/o clips 0 0 0 0 0 > =========================================================================== > > > Starting clips: done. > Clipping: requested bad sequence search clip and a minimum left clip > Need to perform minimum left clip before bad sequence search clip. > Starting minimum left clip ... done. > Performing search for bad sequence quality ... done. > C1530710_1: unable to load or other reason for invalid data. > > =========================================================================== > Pool statistics: > Backbones: 15 Backbone rails: 18711 > > Sanger 454 PacBio Solexa SOLiD > ---------------------------------------- > Total reads 61411 0 0 0 0 > Reads wo qual 61411 0 0 0 0 > Used reads 56244 0 0 0 0 > Avg tot rlen 2109 0 0 0 0 > Avg rlen used 2263 0 0 0 0 > > With strain 61411 0 0 0 0 > W/o clips 0 0 0 0 0 > =========================================================================== > > > > Log directory is not on a NFS mount, good. > > Hash analysis for proposed cutbacks:Localtime: Thu May 5 16:10:01 2011 > Writing temporary hstat files: > [0%] ... > > ========================== Memory self assessment > ============================== > Running in 64 bit mode. > > Dump from /proc/meminfo > > -------------------------------------------------------------------------------- > MemTotal: 49448756 kB > MemFree: 16608868 kB > Buffers: 298124 kB > Cached: 13490800 kB > SwapCached: 0 kB > Active: 19048504 kB > Inactive: 13374404 kB > HighTotal: 0 kB > HighFree: 0 kB > LowTotal: 49448756 kB > LowFree: 16608868 kB > SwapTotal: 10482404 kB > SwapFree: 10482404 kB > Dirty: 320772 kB > Writeback: 292 kB > AnonPages: 18634020 kB > Mapped: 15488 kB > Slab: 247892 kB > PageTables: 39756 kB > NFS_Unstable: 0 kB > Bounce: 0 kB > CommitLimit: 56469744 kB > Committed_AS: 18802392 kB > VmallocTotal: 34359738367 kB > VmallocUsed: 278268 kB > VmallocChunk: 34359434479 kB > HugePages_Total: 0 > HugePages_Free: 0 > HugePages_Rsvd: 0 > Hugepagesize: 2048 kB > > -------------------------------------------------------------------------------- > > Dump from /proc/self/status > > -------------------------------------------------------------------------------- > Name: mira > State: R (running) > SleepAVG: 77% > Tgid: 4568 > Pid: 4568 > PPid: 4565 > TracerPid: 0 > Uid: 610 610 610 610 > Gid: 522 522 522 522 > FDSize: 256 > Groups: 522 > VmPeak: 18182660 kB > VmSize: 18182660 kB > VmLck: 0 kB > VmHWM: 18154484 kB > VmRSS: 18154484 kB > VmData: 18154632 kB > VmStk: 92 kB > VmExe: 3000 kB > VmLib: 4312 kB > VmPTE: 35584 kB > StaBrk: 00916000 kB > Brk: 3b3ed1000 kB > StaStk: 7fffffffdb10 kB > Threads: 1 > SigQ: 0/401408 > SigPnd: 0000000000000000 > ShdPnd: 0000000000000000 > SigBlk: 0000000000000000 > SigIgn: 0000000000001000 > SigCgt: 0000000180000000 > CapInh: 0000000000000000 > CapPrm: 0000000000000000 > CapEff: 0000000000000000 > Cpus_allowed: > 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000008 > Mems_allowed: 00000000,00000003 > > -------------------------------------------------------------------------------- > > Information on current assembly object: > > AS_readpool: 80137 reads. > AS_contigs: 0 contigs. > AS_bbcontigs: 15 contigs. > Mem used for reads: 5743048088 (5.3 GiB) > > 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 4 MiB 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: 80137 313 KiB 0 B 4 B > AS_clipright: 80137 313 KiB 0 B 4 B > AS_used_ids: 80137 78 KiB 0 B 7 B > AS_multicopies: 0 78 KiB 78 KiB 7 B > AS_hasmcoverlaps: 0 78 KiB 78 KiB 7 B > AS_maxcoveragereached: 80137 313 KiB 0 B 4 B > AS_coverageperseqtype: 0 24 B 0 B 0 B > AS_istroublemaker: 80137 78 KiB 0 B 7 B > AS_isdebris: 80137 78 KiB 0 B 7 B > AS_needalloverlaps: 80137 78 KiB 55 B 0 B > AS_readsforrepeatresolve: 0 40 B 0 B 0 B > AS_allrmbsok: 0 313 KiB 313 KiB 4 B > AS_probablermbsnotok: 0 313 KiB 313 KiB 4 B > AS_weakrmbsnotok: 0 313 KiB 313 KiB 4 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: 4 144 B 0 B 0 B > Total: 5749299792 (5.4 GiB) > > > ================================================================================ > Dynamic allocs: 0 > Align allocs: 0 > > Fatal error (may be due to problems of the input data or parameters): > > "Read rr_####2568#### is longer than MAXREADSIZEALLOWED (29900) bases. Skim > cannot handle than, sorry." > > ->Thrown: void Skim::transformSeqToVariableHash (...) > ->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. > > CWD: /vlsci/VR0013/rtgood/data/712soap > Thank you for noticing that this is *NOT* a crash, but a > controlled program stop. > > > -- > You have received this mail because you are subscribed to the mira_talk > mailing list. For information on how to subscribe or unsubscribe, please > visit http://www.chevreux.org/mira_mailinglists.html >