Hello Aaron,
Thank you for your thorough reply. I do have access to UW's CHTC network. So,
if I run progressivemauve distantly on Condor can I then visualize the outputs
locally? Thanks again for this program. I'm attempting to align a de novo
(Spades) assembly of an insect with its sister species and compare the outputs
with a BWA using the same data.
Go Badgers,
Zach
PS If academia doesn't work out there's always comedy!
________________________________
From: Aaron Darling <aaron.darl...@uts.edu.au>
Sent: Tuesday, October 4, 2016 4:47:51 AM
To: Rose Mark USRE; ZACHARY COHEN; mauve-users@lists.sourceforge.net
Subject: Re: [Mauve-users] Crap. It's broke.
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:zcoh...@wisc.edu]
Sent: Sunday, October 02, 2016 11:12 PM
To: mauve-users@lists.sourceforge.net
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
Mauve-users@lists.sourceforge.net<mailto:Mauve-users@lists.sourceforge.net>
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
Mauve-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mauve-users
