[maker-devel] Patch for a bug with repeat gff

[Carson Holt]

Could you send me your repeat_gff and genome fasta, so I can take a look.

Thanks,
Carson



On 13-06-11 11:03 AM, "Anthony Bretaudeau"
<anthony.bretaudeau at rennes.inra.fr> wrote:

>Hello,
>I have just tested with 2.28b: the problem is still there, and my fix
>works on this version too.
>Cheers
>Anthony
>
>On 10/06/2013 18:13, Carson Holt wrote:
>> Could you use MAKER version 2.28 instead (launch with maker -a if it
>>still
>> fails).
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 13-06-10 11:48 AM, "Anthony Bretaudeau"
>> <anthony.bretaudeau at rennes.inra.fr> wrote:
>>
>>> Hello,
>>> I am running Maker 2.27b on an insect genome, and I use a gff file
>>> containing some repeat positions (rm_gff option in maker_opts.ctl).
>>>
>>> I encountered an error on 10 scaffolds (the genome contains ~40000
>>> scaffolds) : "substr outside of string" (similar to this post:
>>> 
>>>http://gmod.827538.n3.nabble.com/substr-outside-of-string-td4031889.html
>>>).
>>>
>>> After a lot a debugging, it turns out the problem came from the code of
>>> "phathits_on_chunk" function in lib/GFFDB.pm, near line 539: there is a
>>> SQL query that fetches features that overlap with the border of the
>>> sequence chunk.
>>> The problem is that it also fetches features that are completely
>>>outside
>>> of the chunk in the same region. This produces an error when maker
>>>tries
>>> to mask the sequence as it does a substr outside the string.
>>>
>>> I fixed it by patching lib/repeat_mask_seq.pm, near line 138:
>>> I replaced:
>>>            substr($$seq, $b -1 , $l, "$replace"x$l);
>>> By:
>>>        if ($b < length($$seq)) {
>>>            substr($$seq, $b -1 , $l, "$replace"x$l);
>>>        }
>>>
>>> I don't know if there is a more elegant solution, but this seems to
>>> solve the problem.
>>>
>>> Cheers
>>> Anthony
>>>
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>>
>