Re: [Mauve-users] Crap. It's broke.
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koadman
From: Aaron D. <aar...@ut...> - 2016-10-04 10:04:06
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Hi Zachary, Mark, et al, Glad you are able to see some humor in these error messages! Zachary, thanks for sending the log file. From that it looks like you are attempting an alignment of genomes that are 1.1Gbp and 597Mbp, respectively. It also appears that your computer has about 32GB of RAM, which unfortunately is not enough to build the sorted seed index datastructures in memory. So progressiveMauve is trying instead to build the index on disk, and there appears to be a bug in that very infrequently used functionality. If possible, I suggest getting a machine with a bit more RAM to do your genome alignment. As a rough guess 64GB may be enough, but I can't say with certainty. If that's not readily available in your department it's also possible to rent machines with large memory in the Amazon EC2 cloud, for a price of course. Best, -Aaron On Mon, 2016-10-03 at 17:11 +0000, Rose Mark USRE wrote: > Don’t have an answer but, damn, I respect the candidness of that > error! > > From: ZACHARY COHEN [mailto:zc...@wi...] > Sent: Sunday, October 02, 2016 11:12 PM > To: mau...@li... > Subject: [Mauve-users] Crap. It's broke. > > hello, > > I am trying to use Mauve to align my scaffolds.fa output from a > Spades de novo assembly against a reference, but received an error. > I've attached the error output file for your consideration and would > greatly appreciate any feedback. Thanks again and I hope to hear from > you soon. > > > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and > delete the original and any copies. Any use of the message by you is > prohibited. > ------------------------------------------------------------------- > ----------- > 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. |