[maker-devel] ERROR: RepeatMasker failed

[Jason Stajich]

I think that may be about permissions of creating the all file in your
RepeatMasker library folder - you may look at the write permissions there
and see.


On Tue, Mar 8, 2016 at 12:25 PM Carson Holt <carsonhh at gmail.com> wrote:

> The issue is unrelated to MAKER. Likely something happened during your
> initial configuration that resulted in a partial file. Perhaps when you
> unpackaged RepBase. Whether you ran it inside or outside of MAEKR was not
> the issue.
>
> —Carson
>
>
> On Mar 8, 2016, at 1:22 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
>
> Hi Carson,
>
> Thank you! I re-install the RepeatMasker, and run it with "-species all"
> outside of MAKER. It was successfully finished. Then I run Maker, and there
> is no error. I am curious why RepeatMasker could not build these library
> files when it was run in the MAKER.
>
> Thanks!
>
> Best,
> Wenbo
>
> 2016-03-07 16:54 GMT-05:00 Carson Holt <carsonhh at gmail.com>:
>
>> RepeatMasker doesn’t actually finish installing until after you run it at
>> least once with the RepBase Libraries (i.e. first job with RepBase). During
>> it’s very first run it builds a bunch of needed library files under
>> …/RepeatMasker/Libraries/ or sometimes under ~/.RepeatMaskerCache/. The
>> failure message you get is that it can’t build those files (which is a
>> RepeatMasker error not a MAKER error). So RepeatMasker is either installed
>> or configured incorrectly.
>>
>> —Carson
>>
>>
>>
>> On Mar 7, 2016, at 2:01 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>> Make sure you use the same library you are giving it with MAKER. You can
>> also look at MAKER’s STDERR to see exactly what command MAKER was using to
>> run RepeatMasker.
>>
>> This error —> "RepeatMasker::createLib(): Error invoking
>> /home/chenwb/programs/ncbi-blast-2.2.28+/bin/makeblastdb on file"
>>
>>
>> It’s not from MAKER. RepeatMasker is printing that error and then failing.
>>
>> —Carson
>>
>>
>>
>> On Mar 7, 2016, at 1:26 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
>>
>> Hi Carson,
>>
>> Thank you for your reply. I installed RepeatMasker following
>> the Installation in their website, and got these information below.
>>
>> =============================
>> Congratulations!  RepeatMasker is now ready to use.
>> The program is installed with a full version of the repeat library:
>>   DFAM Library Version = Dfam_2.0
>>   RMLibrary Version = 20150807
>>   Repbase Version = 20150807
>> =============================
>>
>> I run RepeatMasker directly on one scaffold, and got no error. So I am
>> still confused by the error given by MAKER.
>>
>> Thank you!
>>
>> Best,
>> Wenbo
>>
>> 2016-03-06 15:13 GMT-05:00 Carson Holt <carsonhh at gmail.com>:
>>
>>> Hi Wenbo,
>>>
>>> The error is from RepeatMasker and not MAKER. It means that RepeatMasker
>>> is not installed and configured correctly.  You will have to fix whatever
>>> is wrong with your installation, and then make sure you can get
>>> RepeatMasker to run correctly by itself before running it inside of MAKER
>>> (i.e. run RepeatMasker directly on some test data).
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>> > On Mar 5, 2016, at 7:10 PM, 陈文博 <chenwenbo1020 at gmail.com> wrote:
>>> >
>>> > Hi All,
>>> >
>>> > I have run Maker (v2.31.8) successfully. Now I update RepeatMasker to
>>> v4.0.6. then I came with this error:
>>> >
>>> > RepeatMasker::createLib(): Error invoking
>>> /home/chenwb/programs/ncbi-blast-2.2.28+/bin/makeblastdb on file
>>> /home/chenwb/programs/RepeatMasker/Libraries/20150807/general/simple.lib.
>>> > ERROR: RepeatMasker failed
>>> > --> rank=4, hostname=hostname
>>> > ERROR: Failed while doing repeat masking
>>> > ERROR: Chunk failed at level:0, tier_type:1
>>> > FAILED CONTIG:scaffold149
>>> >
>>> >
>>> > The RepeatMasker was corrected installed. Should I update Maker to
>>> V3.0?
>>> >
>>> > Thank you!
>>> >
>>> > Best regards,
>>> > Wenbo
>>> > _______________________________________________
>>> > maker-devel mailing list
>>> > maker-devel at box290.bluehost.com
>>> >
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>
>>
>>
>
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