Re: [Mauve-users] SNP extraction
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From: Aleksander M. <ale...@nl...> - 2016-12-13 16:18:12
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Hi, It worked perfectly from the command line. If the following information will be in any help: I'm running the latest snapshot of Mauve. When working with viewer no error messages appeared in terminal, the log window in viewer did not open. Mauve created a bunch of java jobs and ran them on all available cores and then just stopped after a few minutes with the output remaining empty. Thank you for your help. Best, Aleksander ----- Izvirno sporočilo ----- Od: "aaron darling" <aar...@ut...> Za: "mauve-users" <mau...@li...> Poslano: Torek, 13. December 2016 16:05:28 Zadeva: Re: [Mauve-users] SNP extraction Hi Aleksander, No the guide tree is not used in the SNP extraction. Did your progressiveMauve run generate the .backbone and .bbcols files? Are you generating the SNP file from the command line or within the viewer? Are there any messages in either the terminal or the console log window? Best, -Aaron On Tue, 2016-12-13 at 15:07 +0100, Aleksander Mahnič wrote: > Hi all, > > I have some problems with SNP extraction from alignment of 48 genomes > (the output file remains empty). > I noticed, that we did not set the progressiveMauve to save the guide > tree. Could this play a role in SNP extract failing? > > If so.. Is there a fast option to make a guide tree from the > alignment or is it easier to just run alignment again? > > Thank you. > > Best, > Aleksander > > -- > National Laboratory of Health, Environment and Food (NLZOH) > Prvomajska ulica 1, 2000 Maribor, Slovenia > tel: +386 (0)2 4500 175 > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Mauve-users mailing list Mau...@li... https://lists.sourceforge.net/lists/listinfo/mauve-users |