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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Jul 7 00:06:54 UTC 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.
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