The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static On Wed, Apr 18, 2012 at 3:31 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

On Wed, Apr 18, 2012 at 11:21 PM, JIE CHEN <jiechenable1987@gmail.com> wrote:

...

Dear all,

I just installed Mira-Assembler via Galaxy tool sheds. As expected, it downloaded the wrappers into the "shed-tools" directory. Then I downloaded and installed Mira binaries on the system and add it to $PATH. Right now, mira can run successfully in the command line prompt.

Which version of MIRA did you install?

...

However when i run it in the Galaxy UI, i run into the below error:

Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat SOLEXA_SETTINGS -LR:lsd=1:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1

Anyone know why? Thanks in advance.

Did you get anything in the MIRA log file (it should be in your history with text data even though it will be red as a failed job)?

Peter

Hi Peter, Thank you for your patience. I checked the error message in the history. They all give exactly the same error-- the one i gave in the first thread. I re thinks the procedure many times and it shouldn't have any problem. Don't know why. What i have done: 1. Installed the mira wrappers using the Galaxy web UI and checked that the mira.py and mira.xml is under one of the directories of the shed_tools directory. 2. installed the mira 3.4.0 binaries in my host Thanks a lot. Tyler On Thu, Apr 19, 2012 at 2:11 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

On Thu, Apr 19, 2012 at 12:40 AM, JIE CHEN <jiechenable1987@gmail.com> wrote:

...

The version I installed is : mira_3.4.0_prod_linux-gnu_x86_64_static

OK, good.

The other key question I asked was did you get anything in the MIRA log file (it should be in your history with text data even though it will be red as a failed job)?

Peter

Hi Peter, Here is the full log: 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@freelists.org 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: Linux whsiao-ubuntu 2.6.32-40-generic #87-Ubuntu SMP Tue Mar 6 00:56:56 UTC 2012 x86_64 GNU/Linux Parsing parameters: --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 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) : mira Project name out (proout) : mira 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) : 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) : 0 Wants quality file (wqf) : yes 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) : 4 Skim each pass (sep) : yes Maximum number of RMB break loops (rbl) : 2 Maximum contigs per pass (mcpp) : 0 Minimum read length (mrl) : 80 Minimum reads per contig (mrpc) : 2 Base default quality (bdq) : 10 Enforce presence of qualities (epoq) : yes 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) : no Default strain name (dsn) : 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) : 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 Min qual. threshold for entire read (mqtfer): 0 Number of bases (mqtfernob) : 0 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 Clip 3 prime polybase (c3pp) : no Minimum signal length (c3ppmsl) : 12 Max errors allowed (c3ppmea) : 2 Max gap from ends (c3ppmgfe) : 9 Clip known adaptors right (ckar) : no 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 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) : 65 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) : 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 Max. start cache fill time (mscft) : 5 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) : 17 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) : mira 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 Keep ends unmerged (msrkeu) : -1 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 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 : mira_assembly For writing result files : mira_assembly/mira_d_results For writing result info files : mira_assembly/mira_d_info For writing tmp files : mira_assembly/mira_d_tmp Tmp redirected to (trt) : For writing checkpoint files : mira_assembly/mira_d_chkpt File names (-FN): When loading sequences from FASTA : mira_in.sanger.fasta When loading qualities from FASTA quality : mira_in.sanger.fasta.qual When loading sequences from FASTQ : /media/partition2_/galaxydb_data/000/dataset_290.dat 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.txt When loading XML trace info files : mira_traceinfo_in.sanger.xml When loading SSAHA2 vector screen results : mira_ssaha2vectorscreen_in.txt When loading SMALT vector screen results : mira_smaltvectorscreen_in.txt When 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 GFF3 : mira_backbone_in.gff3 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 tmps (rrot) : yes Remove tmp directory (rtd) : yes Result files: Saved as CAF (orc) : yes Saved as MAF (orm) : no 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) : no 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 : mira_out.caf MAF : mira_out.maf FASTA : mira_out.unpadded.fasta FASTA quality : mira_out.unpadded.fasta.qual FASTA (padded) : mira_out.padded.fasta FASTA qual.(pad): mira_out.padded.fasta.qual GAP4 (directory): mira_out.gap4da ACE : mira_out.ace HTML : mira_out.html Simple text : mira_out.txt TCS overview : mira_out.tcs Wiggle : mira_out.wig ------------------------------------------------------------------------------ Deleting old directory mira_assembly ... done. Creating directory mira_assembly ... done. Creating directory mira_assembly/mira_d_tmp ... done. Creating directory mira_assembly/mira_d_results ... done. Creating directory mira_assembly/mira_d_info ... done. Creating directory mira_assembly/mira_d_chkpt ... done. Tmp directory is not on a NFS mount, good. Localtime: Thu Apr 19 10:53:58 2012 Loading data (Sanger) from FASTQ files, Localtime: Thu Apr 19 10:53:58 2012 Counting sequences in FASTQ file: found 1 sequences. Localtime: Thu Apr 19 10:53:58 2012 Localtime: Thu Apr 19 10:53:58 2012 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 1 reads. Longest Sanger: 36 Longest 454: 0 Longest IonTor: 0 Longest PacBio: 0 Longest Solexa: 0 Longest Solid: 0 Longest overall: 36 Total reads to load: 1 Reserving space for reads Reserved space for 11 reads. Loading data (Sanger) from FASTQ files, Localtime: Thu Apr 19 10:53:58 2012 Counting sequences in FASTQ file: found 1 sequences. Localtime: Thu Apr 19 10:53:58 2012 Using calculated FASTQ quality offset: 104 Localtime: Thu Apr 19 10:53:58 2012 Loading data from FASTQ file: [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%] Done. Loaded 1 reads, Localtime: Thu Apr 19 10:53:58 2012 Localtime: Thu Apr 19 10:53:58 2012 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. 1 SCF files were not found (see 'mira_assembly/mira_d_tmp/mira_info_scfreadfail.0' for a list of names). Loaded 1 Sanger reads. Total reads loaded: 1 Localtime: Thu Apr 19 10:53:58 2012 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. 1 SCF files were not found (see 'mira_assembly/mira_d_tmp/mira_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. 1 reads with valid data for assembly. Localtime: Thu Apr 19 10:53:58 2012 Generated 1 unique template ids for 1 valid reads. No useful template information found, template routines will not be used. Localtime: Thu Apr 19 10:53:58 2012 Generated 0 unique strain ids for 1 reads. Strain "default" has 1 reads. Have read pool with 1 reads. =========================================================================== Pool statistics: Backbones: 0 Backbone rails: 0 Sanger 454 IonTor PacBio Solexa SOLiD ---------------------------------------- Total reads 1 0 0 0 0 0 Reads wo qual 0 0 0 0 0 0 Used reads 0 0 0 0 0 0 Avg tot rlen 36 0 0 0 0 0 Avg rlen used 0 0 0 0 0 0 With strain 0 0 0 0 0 0 W/o clips 0 0 0 0 0 0 Sanger total bases:36 used bases in used reads: 0 454 total bases:0 used bases in used reads: 0 IonTor total bases:0 used bases in used reads: 0 PacBio total bases:0 used bases in used reads: 0 Solexa total bases:0 used bases in used reads: 0 Solid total bases:0 used bases in used reads: 0 =========================================================================== ========================== Memory self assessment ============================== Running in 64 bit mode. Dump from /proc/meminfo -------------------------------------------------------------------------------- MemTotal: 16209628 kB MemFree: 6527928 kB Buffers: 324332 kB Cached: 6344208 kB SwapCached: 424 kB Active: 5900208 kB Inactive: 2224260 kB Active(anon): 1308772 kB Inactive(anon): 179636 kB Active(file): 4591436 kB Inactive(file): 2044624 kB Unevictable: 56 kB Mlocked: 56 kB SwapTotal: 39535608 kB SwapFree: 39531904 kB Dirty: 4292 kB Writeback: 0 kB AnonPages: 1455560 kB Mapped: 187664 kB Shmem: 32480 kB Slab: 326072 kB SReclaimable: 296460 kB SUnreclaim: 29612 kB KernelStack: 4000 kB PageTables: 31452 kB NFS_Unstable: 0 kB Bounce: 0 kB WritebackTmp: 0 kB CommitLimit: 47640420 kB Committed_AS: 3610840 kB VmallocTotal: 34359738367 kB VmallocUsed: 354268 kB VmallocChunk: 34359380860 kB HardwareCorrupted: 0 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 HugePages_Surp: 0 Hugepagesize: 2048 kB DirectMap4k: 2587200 kB DirectMap2M: 13926400 kB DirectMap1G: 0 kB -------------------------------------------------------------------------------- Dump from /proc/self/status -------------------------------------------------------------------------------- Name: mira State: R (running) Tgid: 20591 Pid: 20591 PPid: 20590 TracerPid: 0 Uid: 0 0 0 0 Gid: 0 0 0 0 FDSize: 64 Groups: 0 VmPeak: 11920 kB VmSize: 11916 kB VmLck: 0 kB VmHWM: 7192 kB VmRSS: 7192 kB VmData: 6556 kB VmStk: 88 kB VmExe: 5236 kB VmLib: 0 kB VmPTE: 40 kB Threads: 1 SigQ: 1/16382 SigPnd: 0000000000000000 ShdPnd: 0000000000000000 SigBlk: 0000000000000000 SigIgn: 0000000001001000 SigCgt: 0000000180000000 CapInh: 0000000000000000 CapPrm: ffffffffffffffff CapEff: ffffffffffffffff CapBnd: ffffffffffffffff Cpus_allowed: 3f Cpus_allowed_list: 0-5 Mems_allowed: 00000000,00000001 Mems_allowed_list: 0 voluntary_ctxt_switches: 10 nonvoluntary_ctxt_switches: 4 -------------------------------------------------------------------------------- Information on current assembly object: AS_readpool: 1 reads. AS_contigs: 0 contigs. AS_bbcontigs: 0 contigs. Mem used for reads: 3136 (3 KiB) 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: 1 24 B 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: 0 24 B 0 B 0 B AS_clipright: 0 24 B 0 B 0 B AS_used_ids: 0 24 B 0 B 0 B AS_multicopies: 0 24 B 0 B 0 B AS_hasmcoverlaps: 0 24 B 0 B 0 B AS_maxcoveragereached: 0 24 B 0 B 0 B AS_coverageperseqtype: 0 24 B 0 B 0 B AS_istroublemaker: 0 24 B 0 B 0 B AS_isdebris: 0 24 B 0 B 0 B AS_needalloverlaps: 0 40 B 0 B 0 B AS_readsforrepeatresolve: 0 40 B 0 B 0 B AS_allrmbsok: 0 24 B 0 B 0 B AS_probablermbsnotok: 0 24 B 0 B 0 B AS_weakrmbsnotok: 0 24 B 0 B 0 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_usedtmpfiles: 3 112 B 0 B 0 B Total: 4008 (4 KiB) ================================================================================ Dynamic allocs: 0 Align allocs: 0 Fatal error (may be due to problems of the input data or parameters): "No read can be used for assembly." ->Thrown: void Assembly::dumpSomeStatistics() ->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: http://www.freelists.org/list/mira_talk CWD: /usr/local/projects/galaxy-dist/database/job_working_directory/000/253 Thank you for noticing that this is *NOT* a crash, but a controlled program stop. MIRA took 0.00 minutes Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 Thanks, Tyler On Thu, Apr 19, 2012 at 10:48 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

...

Hi Peter,

Thank you for your patience. I checked the error message in the history. They all give exactly the same error-- the one i gave in the first

On Thu, Apr 19, 2012 at 6:35 PM, JIE CHEN <jiechenable1987@gmail.com> wrote: thread.

Are you saying this is the entire contents of the MIRA log entry in the history?

Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat SOLEXA_SETTINGS -LR:lsd=1:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1

I'm pretty sure you are just telling me the error message. I would have expected more than that, e.g. a line "MIRA took XXX minutes" before that error message.

To try to be even clearer:

1. Start your web browser and goto your Galaxy 2. Upload/import the files 3. Select the MIRA tool from left hand pane 4. Select input files and set parameters 5. Click "Execute" 6. Notice that six new history entries appear: MIRA contigs (FASTA), MIRA contigs (QUAL)",MIRA contigs (CAF), MIRA contigs (ACE)", MIRA coverage (Wiggle), MIRA log 7. Wait for MIRA to fail and the six new history entries to go red. 8. Click on the "eye" icon for the red history item "MIRA log" 9. Copy and paste the MIRA log contents to an email.

Also, and perhaps equally useful, can you access this server at the command line and try the exact same failing command (from a temp directory - it may create lots of files and folders)?

Peter

Thank you Peter. I changed the dataset and succeeded this time. Appreciated for you help. Cheers, Tyler On Thu, Apr 19, 2012 at 12:40 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

On Thu, Apr 19, 2012 at 7:13 PM, JIE CHEN <jiechenable1987@gmail.com> wrote:

...

Hi Peter,

Here is the full log:

Excellent :)

The good news is MIRA seems to be installed and running fine - it just didn't like your test data, and I understand why:

...

...

Sanger will load 1 reads. Longest Sanger: 36 Longest 454: 0 Longest IonTor: 0 Longest PacBio: 0 Longest Solexa: 0 Longest Solid: 0 Longest overall: 36 Total reads to load: 1 ... Sanger total bases:36 used bases in used reads: 0 454 total bases:0 used bases in used reads: 0 IonTor total bases:0 used bases in used reads: 0 PacBio total bases:0 used bases in used reads: 0 Solexa total bases:0 used bases in used reads: 0 Solid total bases:0 used bases in used reads: 0

..

Fatal error (may be due to problems of the input data or parameters):

"No read can be used for assembly."

...

Then finally some information my wrapper script adds:

...

MIRA took 0.00 minutes Return error code 1 from command: mira --job=denovo,genome,accurate SANGER_SETTINGS -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat COMMON_SETTINGS -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1

It appears you are trying to run MIRA with a single 36bp read, telling MIRA this is a Sanger read. That is very odd (not least because a 36bp read sounds more likely to be an early Solexa/Illumina read from the length).

Has something gone wrong with loading the data into Galaxy? Or did you just want to try a trivial test case? If so, it was too simple and MIRA has stopped because it thinks it is bad input.

The MIRA output log file (which is actually written to the stout if you run MIRA yourself at the command line) is quite verbose, but it is incredibly useful for diagnosing problems. That is why I collect it as one of the output files in Galaxy.

You should be able to try some larger realistic examples, e.g. a virus or a bacterial genome depending on your server's capabilities. And if they fail, have a look through the log file for why MIRA said it failed.

Also keep in mind that the Galaxy wrapper is deliberately a simplified front end - MIRA has dozens of command line options which are not available via my wrapper for simplicity.

Regards,

Peter