Attached please find the log file. I do not understand (i)The NFS system. How do I modify the assembly command to redirect the tmp directory somewhere else (ii)What is SSD (iii)Why is mira also using Sanger files/data when I am not assembling sander data? Thank you. Regards Archana -----Original Message----- From: Chauhan, Archana Sent: Thursday, April 12, 2012 9:27 AM To: 'mira_talk@xxxxxxxxxxxxx' Subject: RE: mira_talk Digest V5 #65 Hi Chevreux, The details of the los _assembly files are as under: ******************************************************************************* [Newton:psi00b HK44_assembly]$ vi log_assembly 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: Linux psi00a 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 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 "log_assembly" 486L, 22794C ********************************************************************************************************************** Regards, Archie -----Original Message----- From: FreeLists Mailing List Manager [mailto:ecartis@xxxxxxxxxxxxx] Sent: Thursday, April 12, 2012 1:14 AM To: mira_talk digest users Subject: mira_talk Digest V5 #65 mira_talk Digest Wed, 11 Apr 2012 Volume: 05 Issue: 065 In This Issue: [mira_talk] mira not assembling [mira_talk] Re: mira not assembling [mira_talk] =?utf-8?B?UmU6IFttaXJhX3RhbGtdIG1pcmEgIG5vdCBhc3 ---------------------------------------------------------------------- From: "Chauhan, Archana" <achauha1@xxxxxxx> Subject: [mira_talk] mira not assembling Date: Wed, 11 Apr 2012 18:10:35 +0000 Hi, I am using mira for the first time. I am trying to assemble my 454 unpaired and paired end reads with mira. I could successfully extracted the both the unpaired and the paired end data from respective . sff files. Now I am trying to run the assembly with following command: mira --project=HK44 --jobÞnovo,genome,454 >&log_assembly [Newton:psi00a data]$ sff_extract -o HK44 ../origdata/FPBW0DM01.sff Working on '../origdata/FPBW0DM01.sff': Converting '../origdata/FPBW0DM01.sff' ... done. Converted 617042 reads into 617042 sequences. [Newton:psi00a data]$ ls -l total 1108371 -rw-r--r--+ 1 achauha1 users 326954919 Apr 11 13:51 HK44.fasta -rw-r--r--+ 1 achauha1 users 957040435 Apr 11 13:51 HK44.fasta.qual -rw-r--r--+ 1 achauha1 users 103997244 Apr 11 13:51 HK44.xml [Newton:psi00a data]$ head -40 HK44.fasta | grep -v ">" | cut -c 1-30 tcagTGCCAGTGCTCGACCGAAGCGTCTGT tcagGTTGACTATTGAGTCGCCACCTGCGC tcagTGTCGAAATTGACCCCGGAACACACT tcagCGCTGCGCTTGGCAACTTGAGCGCTT tcagTTGCAGGGATCGCCCATGAAGCGCTT tcagCGCAGTAGATTGCGAGCATCAAGCAC tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagAGATGACTGCCATTCCTACCGCGACC tcagAATCCAGGTTCTTCGAATGGCAGAAT tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagTCGCCATGCTCATGCAATGCCGCGTC tcagGACCTTGGCATCCAGCGCGCCAAGGT tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagTTCAGGCCGAATCGAAGCATTGGGAC tcagGTCTTGGCGCCGTGCTTGCCGATGTG tcagCTGGTAGAGAAGCACGTGCCAAGGCA tcagTTCAGATCCGCTGGCGACAGCGGTCC tcagAAGTCCGGCTCCATCAGCAGCAGGCC tcagCGTCGCGCATCGCTGCAACGTTATCT tcagTTTTTATCGCTTTCGGTCAACGTAAA [Newton:psi00a data]$ cat ../origdata/linker.fasta >titlinker1 TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG >titlinker2 CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA [Newton:psi00a data]$ sff_extract -o HK44 -a -l ../origdata/linker.fasta -i "insert_size:3000,insert_stdev:900" ../origdata/GFW0S2V01.sff Working on '../origdata/GFW0S2V01.sff': Creating temporary sequences from reads in '../origdata/GFW0S2V01.sff' ... insert_size:3000,insert_stdev:900" ./origdata/GFW0S2V01.sff done. Testing whether SSAHA2 is installed and can be launched ... ok. Searching linker sequences with SSAHA2 (this may take a while) ... ok. Parsing SSAHA2 result file ... done. Converting '../origdata/GFW0S2V01.sff' ... done. Converted 263887 reads into 481730 sequences. [Newton:psi00a data]$ ls -l total 1743865 -rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44.fasta -rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 HK44.fasta.qual -rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59 HK44.xml [Newton:psi00a data]$ mv HK44.fasta HK44_in.454.fasta [Newton:psi00a data]$ mv HK44.fasta.qual HK44_in.454.fasta.qual [Newton:psi00a data]$ mv HK44.xml HK44_traceinfo_in.454.xml [Newton:psi00a data]$ ls -l total 1834191 -rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44_in.454.fasta -rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 -rw-r--r--+ HK44_in.454.fasta.qual -rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59 -rw-r--r--+ HK44_traceinfo_in.454.xml [Newton:psi00a data]$ cd ../assembly/ [Newton:psi00a assembly]$ mkdir [Newton:psi00a assembly]$ mkdir arc_041112 [Newton:psi00a assembly]$ ls arc_041112 [Newton:psi00a assembly]$ cd arc_041112/ [Newton:psi00a arc_041112]$ ln -s ../../data/* . [Newton:psi00a arc_041112]$ ls HK44_in.454.fasta HK44_in.454.fasta.qual HK44_traceinfo_in.454.xml [Newton:psi00a arc_041112]$ ls -l total 2 lrwxrwxrwx 1 achauha1 users 28 Apr 11 14:04 HK44_in.454.fasta -> ../../data/HK44_in.454.fasta lrwxrwxrwx 1 achauha1 users 33 Apr 11 14:04 HK44_in.454.fasta.qual -> ../../data/HK44_in.454.fasta.qual lrwxrwxrwx 1 achauha1 users 36 Apr 11 14:04 HK44_traceinfo_in.454.xml -> ../../data/HK44_traceinfo_in.454.xml [Newton:psi00a arc_041112]$ mira --project=HK44 --jobÞnovo,genome,accurate,454 >&log_assembly [Newton:psi00a arc_041112]$ mira --project=HK44 --jobÞnovo,genome,accurate,454 >&log_assembly [Newton:psi00a arc_041112]$ ls HK44_assembly HK44_in.454.fasta HK44_in.454.fasta.qual HK44_traceinfo_in.454.xml log_assembly [Newton:psi00a arc_041112]$ cd HK44_assembly/ [Newton:psi00a HK44_assembly]$ ls -l total 8 drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_chkpt drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_info drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_results drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_tmp [Newton:psi00a HK44_assembly]$ cd HK44_d_results/ [Newton:psi00a HK44_d_results]$ ls [Newton:psi00a HK44_d_results]$ ls -l total 0 [Newton:psi00a HK44_d_results]$ The assembly command creates following subdirectories in the directory "arc_04/11_12" but all are empty. It appears that mira is not assembling (as the command finishes in 2-3 sec only) but does not give any errors either. I am not able to figure out what is going wrong. I wd appreciate if you could guide me. Regards, Archie ------------------------------ From: Bastien Chevreux <bach@xxxxxxxxxxxx> Subject: [mira_talk] Re: mira not assembling Date: Wed, 11 Apr 2012 20:37:55 +0200 On Apr 11, 2012, at 20:10 , Chauhan, Archana wrote: > The assembly command creates following subdirectories in the directory > “arc_04/11_12” but all are empty. It appears that mira is not assembling (as > the command finishes in 2-3 sec only) but does not give any errors either. > > I am not able to figure out what is going wrong. I wd appreciate if you could > guide me. At first glance things should be working. Can you please post "log_assembly" for me to have a look at? B. ------------------------------ Date: 12 Apr 2012 04:28:12 -0000 Subject: [mira_talk] =?utf-8?B?UmU6IFttaXJhX3RhbGtdIG1pcmEgIG5vdCBhc3NlbWJsaW5n From: "Abhishek sharma" <abhishek_btbin@xxxxxxxxxxxxxx> send ur log file .... check out ur files are properly extracted From: "Chauhan, Archana" <achauha1@xxxxxxx> Sent: Wed, 11 Apr 2012 23:41:21 To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx> Subject: [mira_talk] mira not assembling Hi, I am using mira for the first time. I am trying to assemble my 454 unpaired and paired end reads with mira. I could successfully extracted the both the unpaired and the paired end data from respective . sff files. Now I am trying to run the assembly with following command: mira --project=HK44 --job=denovo,genome,454 >&log_assembly [Newton:psi00a data]$ sff_extract -o HK44 ../origdata/FPBW0DM01.sff Working on '../origdata/FPBW0DM01.sff': Converting '../origdata/FPBW0DM01.sff' ... done. Converted 617042 reads into 617042 sequences. [Newton:psi00a data]$ ls -l total 1108371 -rw-r--r--+ 1 achauha1 users 326954919 Apr 11 13:51 HK44.fasta -rw-r--r--+ 1 achauha1 users 957040435 Apr 11 13:51 HK44.fasta.qual -rw-r--r--+ 1 achauha1 users 103997244 Apr 11 13:51 HK44.xml [Newton:psi00a data]$ head -40 HK44.fasta | grep -v ">" | cut -c 1-30 tcagTGCCAGTGCTCGACCGAAGCGTCTGT tcagGTTGACTATTGAGTCGCCACCTGCGC tcagTGTCGAAATTGACCCCGGAACACACT tcagCGCTGCGCTTGGCAACTTGAGCGCTT tcagTTGCAGGGATCGCCCATGAAGCGCTT tcagCGCAGTAGATTGCGAGCATCAAGCAC tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagAGATGACTGCCATTCCTACCGCGACC tcagAATCCAGGTTCTTCGAATGGCAGAAT tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagTCGCCATGCTCATGCAATGCCGCGTC tcagGACCTTGGCATCCAGCGCGCCAAGGT tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagTTCAGGCCGAATCGAAGCATTGGGAC tcagGTCTTGGCGCCGTGCTTGCCGATGTG tcagCTGGTAGAGAAGCACGTGCCAAGGCA tcagTTCAGATCCGCTGGCGACAGCGGTCC tcagAAGTCCGGCTCCATCAGCAGCAGGCC tcagCGTCGCGCATCGCTGCAACGTTATCT tcagTTTTTATCGCTTTCGGTCAACGTAAA [Newton:psi00a data]$ cat ../origdata/linker.fasta >titlinker1 TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG >titlinker2 CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA [Newton:psi00a data]$ sff_extract -o HK44 -a -l ../origdata/linker.fasta -i "insert_size:3000,insert_stdev:900" ../origdata/GFW0S2V01.sff Working on '../origdata/GFW0S2V01.sff': Creating temporary sequences from reads in '../origdata/GFW0S2V01.sff' ... insert_size:3000,insert_stdev:900" ./origdata/GFW0S2V01.sff done. Testing whether SSAHA2 is installed and can be launched ... ok. Searching linker sequences with SSAHA2 (this may take a while) ... ok. Parsing SSAHA2 result file ... done. Converting '../origdata/GFW0S2V01.sff' ... done. Converted 263887 reads into 481730 sequences. [Newton:psi00a data]$ ls -l total 1743865 -rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44.fasta -rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 HK44.fasta.qual -rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59 HK44.xml [Newton:psi00a data]$ mv HK44.fasta HK44_in.454.fasta [Newton:psi00a data]$ mv HK44.fasta.qual HK44_in.454.fasta.qual [Newton:psi00a data]$ mv HK44.xml HK44_traceinfo_in.454.xml [Newton:psi00a data]$ ls -l total 1834191 -rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 -rw-r--r--+ HK44_in.454.fasta -rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 -rw-r--r--+ HK44_in.454.fasta.qual -rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59 -rw-r--r--+ HK44_traceinfo_in.454.xml [Newton:psi00a data]$ cd ../assembly/ [Newton:psi00a assembly]$ mkdir [Newton:psi00a assembly]$ mkdir arc_041112 [Newton:psi00a assembly]$ ls arc_041112 [Newton:psi00a assembly]$ cd arc_041112/ [Newton:psi00a arc_041112]$ ln -s ../../data/* . [Newton:psi00a arc_041112]$ ls HK44_in.454.fasta HK44_in.454.fasta.qual HK44_traceinfo_in.454.xml [Newton:psi00a arc_041112]$ ls -l total 2 lrwxrwxrwx 1 achauha1 users 28 Apr 11 14:04 HK44_in.454.fasta -> ../../data/HK44_in.454.fasta lrwxrwxrwx 1 achauha1 users 33 Apr 11 14:04 HK44_in.454.fasta.qual -> ../../data/HK44_in.454.fasta.qual lrwxrwxrwx 1 achauha1 users 36 Apr 11 14:04 HK44_traceinfo_in.454.xml -> ../../data/HK44_traceinfo_in.454.xml [Newton:psi00a arc_041112]$ mira --project=HK44 --job=denovo,genome,accurate,454 >&log_assembly [Newton:psi00a arc_041112]$ mira --project=HK44 --job=denovo,genome,accurate,454 >&log_assembly [Newton:psi00a arc_041112]$ ls HK44_assembly HK44_in.454.fasta HK44_in.454.fasta.qual HK44_traceinfo_in.454.xml log_assembly [Newton:psi00a arc_041112]$ cd HK44_assembly/ [Newton:psi00a HK44_assembly]$ ls -l total 8 drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_chkpt drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_info drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_results drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_tmp [Newton:psi00a HK44_assembly]$ cd HK44_d_results/ [Newton:psi00a HK44_d_results]$ ls [Newton:psi00a HK44_d_results]$ ls -l total 0 [Newton:psi00a HK44_d_results]$ The assembly command creates following subdirectories in the directory “arc_04/11_12†but all are empty. It appears that mira is not assembling (as the command finishes in 2-3 sec only) but does not give any errors either. I am not able to figure out what is going wrong. I wd appreciate if you could guide me. Regards, Archie ------------------------------ End of mira_talk Digest V5 #65 ******************************
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: Linux psi00a 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 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 : HK44_assembly/HK44_d_tmp 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 sequences 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 HK44_assembly/HK44_d_tmp ... done. Creating directory HK44_assembly/HK44_d_results ... done. Creating directory HK44_assembly/HK44_d_info ... done. Creating directory HK44_assembly/HK44_d_chkpt ... done. 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. Fatal error (may be due to problems of the input data or parameters): "Tmp directory is on a NFS mount ... but we don't want that." ->Thrown: void Assembly::checkForNFSMountOnTmpDir() ->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/HK44/assembly/arc_041112 Thank you for noticing that this is *NOT* a crash, but a controlled program stop.