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." ->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