Problem of maker?

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Problem of maker?

陈军辉(Junhui Chen)

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: [hidden email]

 

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Re: Problem of maker?

Carson Holt-2
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) <[hidden email]> 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
 
<image001.jpg>

邮件声明
本邮件仅为指定的收件者使用,其中可能包含保密的、专有的或享有合法特权的信息。若您并非指定的收件人,请勿使用、保留、泄露、转发、打印、复印本电子邮件或依据本邮件的内容而采取其他行动。如果您误收到本电子邮件,请立即与发送者联系,并请立即从邮箱及其他存储设备中删除这封邮件。谢谢!
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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