From: Salvador R. <sr...@pr...> - 2009-02-04 15:43:56
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Hello, Thanks for your responses. I still have been unable to successfully run this program. I just would like to assemble a lot of reads against a genome of a target organism. I have both the short reads and the genome target in fasta format. According with documentation, I should use AMOScmp, which has the qual file only as an optional argument. However when I run this program without the qual file then I get on the log a lot of ---------------------------- "AFG ERROR: Sequence and quality lengths disagree could not parse 'RED' message with iid:1, message ignored" ---------------------------- and then the program exits with this error: ---------------------------- "bank-transact -c -z -b test.bnk -m test.afg exited with status: 1" ---------------------------- I tried to use tarchive2amos as suggested but I get the following: ---------------------------- tarchive2amos -o test test.txt (test.txt is my fasta with reads) Collecting file information Died at /usr/local/lib/AMOS/AmosFoundation.pm line 272. ---------------------------- Then I got the qual file from our sequencing service.. and I tried to use it, but I get the same error as I would not use that option. I suppose I am doing something bad, which is not related with the qual but I still can't figure out what could be my problem. I am giving up... Thanks anyway. ---sram Adam Phillippy escribió: > Hello Salvador, > Please reference the documentation Lionel kindly pointed to for > tarchive2amos. This program will generate default quality values of 20 > for all bases if you do not have a quality file. The only module of > the AMOS pipelines that uses the quality values is the consensus > generation tool. With all quality values equal, it will call bases by > majority rule rather than the typical probability model. With deep > enough sequencing coverage, this is usually sufficient. > > Best, > Adam > > > On Mon, Feb 2, 2009 at 3:02 PM, Salvador Ramirez <sr...@pr... > <mailto:sr...@pr...>> wrote: > > Hi Lionel, > > Thanks for your response. Unfortunetly the authors of AMOS have not > answered my question and also I have not been able to find information > about those quality files: what are they? how do you normally obtain > them? should they come from the sequencing service? > > Thanks in advance. > > ---sram > > Lionel Guy wrote: > > Hi Salvador, > > > > I guess you can generate fake quality scores for your reads, > although > > this might really affect the way the assembler works. > > > > Given that your seq file is like this: > > > > >read1 > > ACGTGTG > > >read2 > > GGCTGCT > > > > you could have a qual file like this: > > > > >read1 > > 30 30 30 30 30 30 30 > > >read2 > > 30 30 30 30 30 30 30 > > > > Alternatively, you may try to experiment with the -gq and -bq > options, > > but I don't know if they actually replace a qual file. For more > info, see: > > http://amos.sourceforge.net/docs/converters/toAmos.html > > > > You may also try the other converter tarchive2amos and its -qual > option: > > http://amos.sourceforge.net/docs/converters/tarchive2amos.html > > > > The authors of AMOS might have some smarter suggestions... > > > > Cheers, > > > > Lionel > > > > On 1 Feb 2009, at 1:29 , Salvador Ramirez wrote: > > > >> Hi Lionel, > >> > >> Thanks for your response. Actually I don't have quality scores > for my > >> reads. What should I do if I just have the fasta file with reads? > >> > >> Thanks, > >> > >> ---sram > >> > >> Lionel Guy escribió: > >>> Hi Salvador, > >>> > >>> Do you have any quality scores associated with your reads? You > will > >>> need a fasta qual file (option -q in toAmos) to use bank-transact: > >>> > >>> toAmos -s test.seq -q test.qual -o test.afg > >>> > >>> I'm not sure you can have it working without quality data. > >>> > >>> HTH, > >>> > >>> Lionel > >>> > >>> On 30 Jan 2009, at 17:17 , Salvador Ramirez wrote: > >>> > >>>> Dear people, > >>>> > >>>> I recently downloaded amos because I need to use > >>>> AMOScmp-shortReads. I followed instructions at > >>>> http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml but I > >>>> get an > >>>> error. Basically what I did is the following: > >>>> > >>>> 1.- To create a file called test.seq with all my reads on > fasta format. > >>>> 2.- To create a file with my reference genome. In particular one > >>>> chromosome fasta sequence which I renamed as test.1con > >>>> 3.- toAmos -s test.seq -o test.afg > >>>> 4.-AMOScmp-shortReads test > >>>> > >>>> entonces el programa se ejecuta pero arroja el mensaje de error: > >>>> > >>>> bank-transact -c -z -b test.bnk -m test.afg exited with status: 1 > >>>> > >>>> Also, in the test.runAmos.log first appeared a lot of errors: > >>>> --------------------- > >>>> START DATE: Fri Jan 30 08:27:15 2009 > >>>> Bank is: test.bnk > >>>> 0% 100% > >>>> AFG ERROR: Sequence and quality lengths disagree > >>>> could not parse 'RED' message with iid:1, message ignored > >>>> ERROR: Sequence and quality lengths disagree > >>>> could not parse 'RED' message with iid:2, message ignored > >>>> ERROR: Sequence and quality lengths disagree > >>>> could not parse 'RED' message with iid:3, message ignored > >>>> ------------------- > >>>> > >>>> and finally the previously mentioned error. > >>>> I wonder if I am doing something wrong. > >>>> > >>>> Thanks for your time. > >>>> Best, > >>>> > >>>> ---sram > >>> > >> > > > > ============================================ > > Lionel Guy > > Thunmansgatan 25, SE-75421 Uppsala > > > > phone: +46 (0)18 245596 > > mobile: +46 (0)73 9760618 > > email: guy...@gm... <mailto:guy...@gm...> > > ============================================ > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > AMOS-help mailing list > AMO...@li... > <mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-help > > |