Hi AnnalisaIt isn't unusual for this to run for a week. As long as you aren't getting any errors, it's probably working.
Peter On 06/08/2016 6:29 AM, annalisa giampetruzzi wrote:
Dear Prof. Aaron Darling and Mauve users, I'm writing to you to ask some questions about the use of progressiveMauve. The topic of my work is to do a whole genome phylogeny and analyze (by ClonalOrigin) the recombination fluxes on a set of 27 whole genome sequences of bacteria, but most of them consist of contigs, since they are still in draft form. So I have installed Mauve in my linux64 server and I'm trying to launch progressiveMauve on 27 multifasta file. So the my first question is: Does progressiveMauve works fine on genome consisting of contigs? or Should I create a concatenamer of contigs in order to obtain only 27 fasta sequences? Then most of my genome sequences contain sequence/contigs annotated as plasmid. About this do you think it is better to run the progressiveMauve on chromosomes and on plasmids separately? Which is your experience? Actually I have already obtained a core_alignment.xmfa (LCB greater than 100) from my first attempt of running, and now I'm waiting for the result of Clonalframe (ClonalFrame -x 10000 -y 10000 -z 10 core_alignment.xmfa core_clonalframe.out.1 > cf_stdout.1 &...) I have launched the jobs 7 days ago but it is still running, so Is it normal that this job take so many time? How I could speed up this job? Thanks if you have the possibility to answer to these my several questions. Best regards Dott.ssa Annalisa Giampetruzzi*Dott.ssa Annalisa Giampetruzzi* Università degli Studi di Bari Aldo Moro Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti Di.S.S.P.A. Via Amendola 165/A 70126 BARI tel. 0805442538 fax. 0805443608 annalisa.giampetru...@uniba.it annalis...@hotmail.it skype giampe79 ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
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------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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