[maker-devel] maker-2.24 fails while preparing evidence clusters

[Carson Holt]

Here are comments from subversion between 2.24 and 2.25


Renaming and minor fixes to some modules
improved gff3_merge script
fix est passthrough bug
made GFFDB module faster

Thanks,
Carson




On 12-07-05 7:22 AM, "Markus Ankenbrand"
<markus.ankenbrand at stud-mail.uni-wuerzburg.de> wrote:

>Hi Carson,
>
>thanks for your response.
>Version 2.25 works without any errors.
>May I have a changelog for 2.25, if available?
>
>Thanks,
>Markus
>
>
>Am 03.07.2012 16:12, schrieb Carson Holt:
>> Have you tried 2.25 to see if the error still occurs in that version?
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-06-28 10:03 AM, "Markus Ankenbrand"
>> <markus.ankenbrand at stud-mail.uni-wuerzburg.de> wrote:
>>
>>> Hi all,
>>>
>>> I'm using maker-2.24 to annotate contigs of a procaryotic organism. I'm
>>> only using coding sequences of a reference species as "altest". Without
>>> any obvious reason annotation fails for some contigs. It seems to have
>>> nothing to do with the contig length. I also tried to run maker with
>>> different reference ESTs and GeneMark. Depending on the setup different
>>> contigs fail.
>>>
>>> In case of failure, the log is:
>>> ...
>>> cleaning clusters....
>>> total clusters:3 now processing 0
>>>    ...processing 0 of 3
>>>    ...processing 1 of 3
>>> total clusters:3 now processing 0
>>> total clusters:3 now processing 0
>>>    ...processing 0 of 2
>>> Can't call method "start" on an undefined valueERROR: Failed while
>>> preparing evidence clusters for annotations
>>> ERROR: Chunk failed at level:0, tier_type:3
>>> FAILED CONTIG:contig1
>>>
>>> ERROR: Chunk failed at level:7, tier_type:0
>>> FAILED CONTIG:contig1
>>>
>>> --Next Contig--
>>> ...
>>>
>>> If someone has any idea how to solve this problem, help would be very
>>> much apriciated.
>>>
>>> Greetings,
>>> Markus
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>