[maker-devel] Problem of maker？

[Carson Holt]

Hi Hui,

1. Make sure you are not using a very old version of MAKER. Current stable version is 2.31.9
2. If you are using GFF3 input as part of your run, then the issue may be in the input GFF3 file (MAKER gets the coordinates from the file you give it).
3. Delete and rerun the contig in question. The lines you gave in your example are missing columns, which may have just been a cut and paste mistake, but if not, then it’s an IO error - failure to print full line - which just needs to be rerun (can sometimes happen with slow NFS file systems).
4. Make sure you have current version of BioPerl (current CPAN version and not BioPerl-live).


The only previous occurrence of a start position issue with MAKER ( https://groups.google.com/forum/#!searchin/maker-devel/start$20position%7Csort:date/maker-devel/Yzn6XTm2aas/J2IOGyWXbVMJ ) involved the use of a very old MAKER installation together with bad installation of some prerequisites.


Thanks,
Carson



> On Dec 13, 2017, at 2:56 AM, 陈军辉(Junhui Chen) <chenjunhui at bgi.com> wrote:
> 
> Dear Dr，
> Gooddays for you.
>  
> Recently, we used maker software to annotate our genome. However, we found that some annoted genes utr region was out of the scaffold as following:
> sc0000223       maker   five_prime_UTR  101136  101159
> sc0000223      0      101142
>  
> Would you like to give us some suggetions and help about this problem?
> Many thanks for your help and suggestions
>  
> Look forward from you.
>  
>  
> Best regards
> Yours, hui
>  
> 陈军辉 信息分析工程师
> 华大基因股份有限公司 
> 通讯地址：深圳市盐田区洪安三街21号华大综合园7栋，518083
> 联系电话：0755-36307095
> 邮箱: chenjunhui at genomics.cn <mailto:chenjunhui at genomics.cn>
>  
> <image001.jpg>
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