/Sharmistha/Bioinfo/Project_data/Cotton_data/mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform$ ls -l total 746472 drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 13:15 Cotton_backbone_in.gbf drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 14:27 cotton_d_info drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 14:27 cotton_d_log drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 14:27 cotton_d_results -rw-r--r-- 1 sharmistha sharmistha 243851317 2009-09-16 11:03 cotton.fasta -rw-r--r-- 1 sharmistha sharmistha 386595241 2009-09-16 10:56 cotton.fastq -rw-r--r-- 1 sharmistha sharmistha 132828265 2009-09-19 12:58 cotton_straindata_in.txt -rw-r--r-- 1 sharmistha sharmistha 293208 2009-10-01 10:44 gossypium.gbf -rw-r--r-- 1 sharmistha sharmistha 22285 2009-10-02 14:27 log_assembly.txt -rw-r--r-- 1 sharmistha sharmistha 0 2009-09-24 11:34 mira I hope this will serve the purpose. Just check out and let me know. Thanks and regards Sharmistha On Fri, Oct 2, 2009 at 2:34 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote: > Can you please copy/paste your folder contents as before, along with the > error message? > L. > > > On 2 Oct 2009, at 10:59 , Sharmista Saha wrote: > > Sorry Lionel, >> >> Things are not working still for me, giving me the same result. >> >> Please if you can find any other reason over the same? >> >> Thanks and regards, >> Sharmistha >> >> >> >> On Fri, Oct 2, 2009 at 2:13 PM, Sharmista Saha < >> sharmistasaha@xxxxxxxxxxxxxx> wrote: >> Thanks !! I will try as you said, >> >> >> mira --project=cotton --job=mapping,genome,accurate,solexa -AS:nop=1 >> -SB:lsd=yes:bsn=cotton_ref:bft=gbf:bbq=30 >&log_assembly.txt >> >> this was the comment I gave!! >> >> anyclue over this please let me know. >> >> >> Thanks and Regards, >> Sharmistha >> >> >> >> >> >> >> On Fri, Oct 2, 2009 at 1:47 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote: >> Hi Sharmista, >> >> At least mira runs now! >> >> First, as far as I know, the Cotton_backbone_in.gbf file is a folder in >> your system, whereas you should have a normal file (where did you read it >> should be a folder containing the gbf file?). Maybe the real file is located >> inside that folder? Thus move the gbf file into the main directory (where >> the other input files are located) >> >> Second, the file names are case-sensitive, so you must have a file called >> "cotton_backbone_in.gbf", not "Cotton_backbone_in.gbf" (note the capital C). >> >> Could you please paste the command you entered? >> >> Hope this helps, >> >> Lionel >> >> >> >> On 2 Oct 2009, at 9:57 , Sharmista Saha wrote: >> >> Hi everyone, >> Now that I have reinstalled mira and reloaded the data in the bin >> directory of mira, now I can run mira, with your guidance. still mira = 0 >> bytes, and log file shows >> >> AS_readpool: 0 reads. >> AS_contigs: 0 contigs. >> AS_bbcontigs: 0 contigs. >> Mem used for reads: 60 (60 B) >> and >> Warning: "cotton_backbone_in.gbf" >> : File not found. >> ->Thrown: GBF::load(const string & gbfin) >> ->Caught: main >> >> why this conclusion, when I already downloaded the respective gb file of >> the cotton data, renamed as .gbf and stored it in the gbf directory as >> directed in the manual. Although ls -l shows me >> >> drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 13:15 >> Cotton_backbone_in.gbf >> drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 13:15 >> cotton_d_info >> drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 13:15 cotton_d_log >> drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 13:15 >> cotton_d_results >> -rw-r--r-- 1 sharmistha sharmistha 243851317 2009-09-16 11:03 cotton.fasta >> -rw-r--r-- 1 sharmistha sharmistha 386595241 2009-09-16 10:56 cotton.fastq >> -rw-r--r-- 1 sharmistha sharmistha 132828265 2009-09-19 12:58 >> cotton_straindata_in.txt >> -rw-r--r-- 1 sharmistha sharmistha 22289 2009-10-02 13:15 >> log_assembly.txt >> -rw-r--r-- 1 sharmistha sharmistha 0 2009-09-24 11:34 mira >> >> but, the respective directory with 4096 bytes, actually contains nothing >> inside it leaving the gbf directory . Mira actually is not running properly >> is my conclusion, I also feel it is not able to read through my ref file, so >> it cannot draw the respective contigs. If so, what is the reason for it? By >> chance if I am wrong, If the flaw lies elsewhere, please can you guide where >> the error actually lies? >> >> Waiting for some interesting replies >> >> Thanks and Regards, >> >> Sharmistha >> >> On Thu, Oct 1, 2009 at 10:46 AM, Sharmista Saha < >> sharmistasaha@xxxxxxxxxxxxxx> wrote: >> Thanks a lot to both Peter and Bjorn. >> >> Regards, >> Sharmistha >> >> >> On Wed, Sep 30, 2009 at 10:00 PM, Bjoern Usadel <usadel@xxxxxxxxxxxxxxxxx> >> wrote: >> Dear Sharmista, >> >> The best bet would probably to contact the relevant PI for the Gossypium >> projects: It seems finished but not yet released. >> >> http://www.jgi.doe.gov/sequencing/statusreporter/psr.php?projectid=16065 >> >> >> Cheers, >> Björn >> >> >> Peter wrote: >> On Wed, Sep 30, 2009 at 4:11 PM, Sharmista Saha >> <sharmistasaha@xxxxxxxxxxxxxx> wrote: >> >> Hi, >> >> @Peter, thank you, for your suggestion, even myself tried with that >> earlier, >> but I do not find Gossypium, where can i get that gb file of the same? >> >> >> You just asked for Arabidopsis thaliana - not cotton ;) >> >> I tried searching the genomes at the NCBI with Entrez for Gossypium, >> but just found two chloroplasts: >> >> http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&term=Gossypium[orgn] >> >> I am not a plant geneticist, so I have no idea if the whole genome has >> been sequenced, and if it has, where else to look for it. >> >> Peter >> >> >> >> -- >> -------------------------------------------------- >> Björn Usadel, PhD >> Max Planck Institute of Molecular Plant Physiology >> AG Integrative Carbon Biology >> Am Muehlenberg 1 >> 14476 Potsdam-Golm >> Tel.: +49 331 5678153 >> email usadel@xxxxxxxxxxxxxxxxx >> http://tinyurl.com/IntegrativeCarbonBiology >> -------------------------------------------------- >> >> >> >> -- >> 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 >> >> >> >> ============================================ >> Lionel Guy >> Thunmansgatan 25, SE-75421 Uppsala >> >> phone: +46 (0)18 245596 >> mobile: +46 (0)73 9760618 >> email: guy.lionel@xxxxxxxxx >> ============================================ >> >> >> >> -- >> 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 >> >> >> > ============================================ > Lionel Guy > Thunmansgatan 25, SE-75421 Uppsala > > phone: +46 (0)18 245596 > mobile: +46 (0)73 9760618 > email: guy.lionel@xxxxxxxxx > ============================================ > > > -- > 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 >