The error in the log file: Fatal Error: "cotton_in.solexa.fasta" : File not found. ->Thrown: void ReadPool::loadDataFromFASTA(const string & filename, const string & qualfilename, const bool generatefilenames, const uint8 seqtype, const uint8 loadaction) ->Caught: Assembly::loadFASTA(const string & fastafile, const string & fastaqualfile, const uint8 readtype, const uint8 loadaction) Program aborted. CWD: /home/sharmistha/Sharmistha/Bioinfo/Project_data/Cotton_data/mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform Thanks and regards, Sharmistha On Fri, Oct 2, 2009 at 3:51 PM, Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx > wrote: > Hi Lionel, > > After following you, this is what I got. > > Aborted > sharmistha@PLEX-1:~/Sharmistha/Bioinfo/Project_data/Cotton_data/mira_3rc2_dev_linux-gnu_i686_32_static/bin/Dataform$ > ls -l > total 746468 > -rw-r--r-- 1 sharmistha sharmistha 293208 2009-10-01 10:44 > cotton_backbone_in.gbf > 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 15:49 cotton_d_info > drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 15:49 cotton_d_log > drwxr-xr-x 2 sharmistha sharmistha 4096 2009-10-02 15:49 > 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 18365 2009-10-02 15:49 > log_assembly.txt > -rw-r--r-- 1 sharmistha sharmistha 0 2009-09-24 11:34 mira > > Now can you tell me the issue. > > Thanks and regards, > Sharmistha > > > On Fri, Oct 2, 2009 at 2:40 PM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote: > >> Rename gossypium.gbf to cotton_backbone_in.gbf: >> >> mv gossypium.gbf cotton_backbone_in.gbf >> >> and try again. If this doesn't work, send again the folder content and the >> error message (in log_assembly.txt) >> >> L. >> >> On 2 Oct 2009, at 11:07 , Sharmista Saha wrote: >> >> /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 >>> >>> >> ============================================ >> 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 >> > >