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.
--Russell
> -----Original Message-----
> From:
bioperl-l-bounces@... [mailto:bioperl-l-
>
bounces@...] On Behalf Of Sendu Bala
> Sent: Tuesday, 7 July 2009 11:43 a.m.
> To:
manchunjohn-ma@...
> Cc:
bioperl-l@...
> 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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>
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