[maker-devel] ERROR: RepeatMasker failed

[Carson Holt]

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 <mailto: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 <mailto: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 <mailto: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
>> > _______________________________________________
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>> 
>> 
> 

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