[maker-devel] RepeatMasker: NCBIBlastSearchEngine::search: Error

[Carson Holt]

You may have to contact RepBase via e-mail to find out how to get the libraries compatible with RepeatMasker 4.0.6 as it looks like they have removed the previous release from the website.

The last release for 4.0.6 was —> repeatmaskerlibraries-20160829.tar.gz

—Carson



> On May 3, 2017, at 9:55 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> You may want to use the previous version of both as the new version may still have hidden bugs.
> 
> —Carson
> 
>> On May 3, 2017, at 9:53 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>> 
>> RepBase and RepeatMasker have changed structure with the new 4.0.7 released two months ago. The new version and RepBase is only compatible with the new version of RepeatMasker. You have to update both (complete reinstall). Or you have to use the previous version of RepeatMasker with the previous version of RepBase.
>> 
>> —Carson
>> 
>> 
>> 
>>> On May 3, 2017, at 6:15 AM, 卢金原Jim <jim03ljy at 126.com <mailto:jim03ljy at 126.com>> wrote:
>>> 
>>> Hi, I'm a newbie of maker.
>>> I met some errors in Repeatmasker step.
>>> 
>>> The error is here:
>>> NCBIBlastSearchEngine::search: Error...compressed subject database (/home/softwares/RepeatMasker/Libraries/20170127/general/is.lib) does not exist!
>>> 
>>> I tried ncbi+blast 2.5.0 version and 2.6.0 version as the path to blast, both have the same error.
>>> And when I use the command as "maker -R", which skips the repeatmasker step, the maker could work.
>>> I checked the former similar errors reported by another user and he solved the problem by  updating the RepBase.
>>> So,
>>>   I deleted and re-installed the RepeatMasker, updated the RepBase,  also installed RMblast.
>>> The error is the same.
>>> 
>>> I'm stuck in the problem now.
>>> Would highly appreciate any help - thanks!
>>> 
>>> Jinyuan Lu
>>> Shanghai Jiao Tong University
>>> No. 800 Dong Chuan Road,Minhang District,  Shanghai, P.R. China
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>> 
> 

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