Hi Federico, Have you tried having a empty file with the name touch 454_muestra2_backbone_in.454.fasta.qual in the folder? If everything fails you can make the quality file easily with sed cat 454_muestra2_backbone_in.454.fasta | sed 's/[atcg]/100/ig' > 454_muestra2_backbone_in.454.fasta.qual Though the a,t,c and g in the name of the reads in the backbone will be changed also. Best regards, Hákon J. > Hi Marina: > > I had it like that from the begging: > > This is the command line that I use: > /aplic/mira-3.0.0/bin/mira -fasta > -project=*454_muestra2*-job=mapping,genome,normal,454 --noclipping=all > --notraceinfo > COMMON_SETTINGS -AS:sd=yes -SK:mnr=no > -SB:lb=yes:bsn=454_muestra2_backbone_in.454.fasta:bbq=100:bft=fasta:abnc=yes:sbuip=2 > > And this the name of the files right now: > 1) 454_muestra2_in.454.fasta > 2) 454_muestra2_in.454.fasta.qual > 3) 454_muestra2_backbone_in.fasta > > And I have changed the backbone as it was before (backbone_in.fasta, but > if > I do this I get the same message as before that it ""Could not find FASTA > quality file 454_muestra2_backbone_in.fasta.qual, using default values for > these reads"" eventhough I use used the -SK:bbq and sbuip parameters to > describe that I have a good quality on the backbone sequence. > > This is the error print out: > Loading backbone from FASTA file: 454_muestra2_backbone_in.fasta (quality: > 454_muestra2_backbone_in.fasta.qual) > Counting sequences in FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Found 1 sequences. > Loading data from FASTA file: > [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] > ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... > [90%] ....|.... [100%] > Could not find FASTA quality file 454_muestra2_backbone_in.fasta.qual, > using > default values for these reads. > > Done. > Loaded 1 reads with 954 raw bases. > 0 reads have quality accounted for. > Postprocessing backbone (this may take a while) > 1 to process > gi|193083133:1381-2334_bb 954 > Localtime: Mon Mar 15 14:08:59 2010 > > Seeing strain 1: "454_muestra2_backbone_in.fasta" > Generated 1 unique strain ids for 1 reads. > Strain "default" has 0 reads. > Strain "454_muestra2_backbone_in.fasta" has 1 reads. > Loading data (454) from FASTA files, > > Fatal Error (may be due to problems of the input data): > "File not found: 454_muestra2_in.454.fasta" > > ->Thrown: size_t ReadPool::loadDataFromFASTA(const string & filename, > const > uint8 loadaction, uint32 & longestread, const bool wantsqualfiletoexist, > const string & qualfilename, const bool generatefilenames, const uint8 > seqtype, const bool sxa_mustconvert) > > ->Caught: Assembly::loadFASTA(const string & fastafile, const string & > fastaqualfile, const uint8 seqtype, const uint8 loadaction) > > Program aborted, 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. > > So I am back to square one, because this is the same error message that I > used to get before changing the files extension. Could you give any other > advice and help me out with it? Thanks again for the help > > Federico > > > > > > > > > > > > > > > > > > > On Mon, Mar 15, 2010 at 12:39 PM, Marina Manrique > <mmanrique@xxxxxxxx>wrote: > >> Hi Federico, >> >> try setting up input file names as follows (replacing miraProjecName >> with >> your real mira project name...) >> >> miraProjectName_backbone_in.fasta >> miraProjectName_in.454.fasta.qual >> miraProjectName_in.454.fasta >> miraProjectName_traceinfo_in.454.xml >> >> Note that for the backbone file you shouldn't name it with >> ~backbone_in.454.fasta >> >> Hope this helps >> >> Marina >> >> Federico Sanchez escribió: >> >> Hi: >> >> Thanks for the quick answer. I just did what you suggeested me. and >> change >> the files to the _in.454.fasta format, for all of them (the quality file >> and >> the backbone too). However I am still getting an error with the backbone >> file ---> >> >> Fatal Error (may be due to problems of the input data): >> "File not found: 454_muestra2_backbone_in.fasta" >> >> ->Thrown: size_t ReadPool::loadDataFromFASTA(const string & filename, >> const >> uint8 loadaction, uint32 & longestread, const bool wantsqualfiletoexist, >> const string & qualfilename, const bool generatefilenames, const uint8 >> seqtype, const bool sxa_mustconvert) >> >> ->Caught: main >> >> Program aborted, 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: /home/homes/users/fsanchez/MIRA_ASSEMBLY >> Aborted >> >> My command line is the same but changing the backbone file to >> backbone_in.454.fasta instead of the 454_muestra2_backbone_in.fasta, >> what >> else could be going wrong? any suggestions?. At the moment I am not able >> to >> download the newer versions of mira but I hope mira 3.0.0 is up for the >> task. >> >> /aplic/mira-3.0.0/bin/mira -fasta -project=454_muestra2 >> -job=mapping,genome,normal,454 --noclipping=all --notraceinfo >> COMMON_SETTINGS -AS:sd=yes -SK:mnr=no >> -SB:lb=yes:bsn=454_muestra2_backbone_in.454.fasta:bbq=100:bft=fasta:abnc=yes >> >> >> Thanks again for the help >> >> >> Federico >> >> >> >> >> >> On Mon, Mar 15, 2010 at 11:36 AM, Jan Paces <hpaces@xxxxxxxxxx> wrote: >> >>> On 03/15/10 04:56, Federico Sanchez wrote: >>> > 1) /aplic/mira-3.0.0/bin/mira -fasta -project=454_muestra2 >>> > -job=mapping,genome,normal,454 --noclipping=all --notraceinfo >>> > COMMON_SETTINGS -AS:sd=yes -SK:mnr=no >>> > -SB:lb=yes:bsn=454_muestra2_backbone_in.fasta:bbq=100:bft=fasta:abnc=yes >>> >>> For mapping, I suggest to use mira-3.0.3, there were some problems >>> with >>> parsing input data in version 3.0.2 a maybe lower as well, I am not >>> sure. >>> >>> As for the error with input files, you need _in.454. in the names - >>> as pointed out by Sven befora I sent this email ;-) >>> >>> Jan >>> >>> -- >>> 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 >>> >> >> >> > -- 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