cjfields at illinois.edu
Wed Jul 15 18:12:32 EDT 2009
Thanks for the update Robert!
On Jul 14, 2009, at 2:42 PM, Robert Hubley wrote:
> Hi Chris,
> Just got back from a conference.
> So the original problem reported ( "Exception ( no such file or
> directory )" ) caused by:
> "Cause: mysequence.masked file (which holds the masked sequence) not
> found when
> no repeats are found in the supplied sequence. This file is not
> created anymore
> when no repeats are found."
> This is still the case, with RepeatMasker at least. We no longer
> create a *.masked file when no repeats are located in the input
> file. This can be checked by looking at the *.out file which in
> these cases will contain only one line:
> "There were no repetitive sequences detected in ...<filename>..."
> In comment #1 of this bugreport a user writes:
> "This may be related to a bug with RepeatMasker and is known to be
> an issue with
> The RepeatMasker authors have been notified about this and
> hopefully will have
> a fix available soon. The question now is, should RepeatMasker.pm
> check for no
> returned results?"
> This refers to a bug in the option processing in RM Version 3.1.6
> ( '-noint' etc. ). This was fixed
> in 3.1.7 and has not returned. So this should no longer be
> impacting any version of bioperl.
> Chris Fields wrote:
>> Sorry about that last post, thought you were reporting a problem
>> not inquiring about one.
>> Here's what we have:
>> Not sure but from the last few reports this is still a problem with
>> RepeatMasker and bioperl. I'll try looking into it from our end.
>> On Jul 7, 2009, at 8:58 AM, Robert Hubley wrote:
>>> This list email as forwarded to us by a colleague. I fixed this
>>> bug awhile back and I just double checked 3.2.8 and don't see any
>>> problems with the options -noint or -lcambig. Could someone help
>>> us determine how this is breaking bio-perl?
>>> |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
>>> |And as of today, they are now at 3.2.8, and the problem is not
>>> |And I don't want my project to be stalled-- any tips for a
>>> ||Perhaps you already know about this, but in RepeatMasker 3.1.6 -
>>> noint ||cannot be used because of error 'Unknown option: noint-
>>> ||This is caused by line 1131 having no space after the "-noint".
>>> ||Likewise, -lcambig on 1128 would probably suffer a similar
>>> ||Will this be fixed in the next version, and how often do you
>>> release new ||versions?
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
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