[maker-devel] ERROR: RepeatMasker failed

[陈文博]

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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