[Bioperl-l] RepeatMasker still did not act upon Bug 2138: Any workarounds?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Jul 6 20:06:54 EDT 2009

Is it the "-noint" bug causing the crash?
We had major problems (with version 3.2.8) where it would stack-dump which I worked around by running it with the "-no_is" option so it doesn't check for bacterial insertion elements.
We've never had a crash after that  :-)

Also, it is open-source so you could fix your own copy if you know what the bugs are. 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Tuesday, 7 July 2009 11:43 a.m.
> To: manchunjohn-ma at uiowa.edu
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] RepeatMasker still did not act upon Bug 2138: Any
> workarounds?
> John M.C. Ma wrote:
> > We have told the guys at RepeatMasker that RM-3.1.6 have a problem
> > causing Bio::Tools::RepeatMasker to crash in November 2006 (Bug 2138).
> > And as of today, they are now at 3.2.8, and the problem is not fixed.
> > And I don't want my project to be stalled-- any tips for a workaround?
> Here's my mail to some RepeatMasker devs that they never replied to:
> -----
> Hi,
> Perhaps you already know about this, but in RepeatMasker 3.1.6 -noint
> cannot be used because of error 'Unknown option: noint-species'.
> This is caused by line 1131 having no space after the "-noint".
> Likewise, -lcambig on 1128 would probably suffer a similar problem.
> Will this be fixed in the next version, and how often do you release new
> versions?
> -----
> If it really is the same bug, it should be easy to fix the latest
> version in the same way yourself.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.

More information about the Bioperl-l mailing list