El 05.04.2016 15:58, Animesh Sharma escribió: > Marina I am using Ray with paired end reads, but wondering if the > defaults work for you? Something like: > > mpiexec -np 64 ./Ray -k 25 -s Cleanup_454/sequences_.fastq -s > Cleanup_ill/output_files/sequences_.fastq -o testK25def > > Regards, > > Ani > > --------------------------"The Answer Lies In The > Genome"-------------------------- > > On Tue, Apr 5, 2016 at 3:36 PM, marina espigares <mesp...@uma.es> > wrote: > >> El 05.04.2016 14:07, Animesh Sharma escribió: >> >> Hi Marina, >> >> Which Ray version and how are you invoking it? If you simply >> assemble >> with -k and -input files, they won't call these other routines. >> >> Regards, >> >> Ani >> >> --------------------------"The Answer Lies In The >> Genome"-------------------------- >> >> On Tue, Apr 5, 2016 at 12:49 PM, marina espigares <mesp...@uma.es> >> wrote: >> >> Hello, >> >> I am using RAY to assembly the transcriptome of the chestnut tree. >> It >> can generate the contigs pretty fast but the program keep working on >> the >> BiologicalAbundances for a long time. What are those files for? It >> that >> affects the assembly results?, it is possible to deactivate? >> >> Thank you >> >> -- >> Marina Espigares >> >> > ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Denovoassembler-users mailing list >> Denovoassembler-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> [1] >> [1] >> >> Links: >> ------ >> [1] >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >> [1] > > Hello Ani, > > I'm using ray/2.3.1, and I call it this way: > > -mpiexec -np 64 Ray -k 25 -s Cleanup_454/sequences_.fastq -s > Cleanup_ill/output_files/sequences_.fastq -route-messages > -connection-type debruijn -routing-graph-degree 4 > > Any suggestion? > > Regards > > Marina > > > > Links: > ------ > [1] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
Ani, thank you for your advise. It works much faster now. I guess all those options were slow down the execution. Best regards Marina -- Marina Espigares ------------------------------------------------------------------------------ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
