[maker-devel] MAKER v3 ERROR: Failed while processing all repeats

[Kapeel Chougule]

Thanks Carson,

It works now. I only had to replace the Repeat Masker perl module and it
ran without any errors.

Best

Kapeel

On Fri, May 4, 2018 at 2:46 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Kapeel,
>
> The failure is caused by the absence of a start or end coordinate (usually
> caused by a BLAST report truncation - there is a BLAST bug supposably fixed
> now where reports were being truncated by BLAST). If you’ve done all the
> updates to installed tools, make sure you aslo set the location of the
> updated tools in maker_exe.ctl and reran the ./configure script for
> RepeatMasker (internal to it’s install directory) or the old tool is likely
> still being used.
>
> Also if that doesn’t fix it, try the following. Use the attached file to
> replace …/maker/lib/Widget/RepeatMasker.pm
>
> There is also an as of yet unfixed RepeatMasker bug where it reports a 0
> value for the start/end coordinate when configured with RMBLAST
> (RepeatMasker uses a 1 based coordinate system, so 0 is not supposed to be
> possible and it only happens with RMBLAST). The change I made to the parser
> is a hack where I have MAKER change the RepeatMasker coordinate to 1
> whenever it sees the invalid 0.
>
> —Carson
>
>
>
>
>
> On May 1, 2018, at 10:16 AM, Kapeel Chougule <kapeelc at gmail.com> wrote:
>
> Hi,
>
> I am using MAKER v3 to update community annotation with new RNA-seq
> evidence data. Part of my problem is that MAKER shows below error when
> repeat masking. I have attached the community annotation gff, maker log and
> maker_opts.ctl for your reference.  I searched for this error  in the
> maker-dev google group and found some hints
> <https://groups.google.com/forum/#!topic/maker-devel/651ka80F3s4> to
> update BLAST to 2.7, rmblast to 2.6 and reconfigure RepeatMasker which I
> did but it still fails with the error. Any help appreciated.
>
> deleted:0 hits
> collecting blastx repeatmasking
> processing all repeats
> in cluster::shadow_cluster...
> Died at /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/
> bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
> --> rank=1, hostname=bnbcompute15.blacknblue.cshl.edu
> ERROR: Failed while processing all repeats
> ERROR: Chunk failed at level:3, tier_type:1
> FAILED CONTIG:Chr06
>
>
> ERROR: Chunk failed at level:2, tier_type:0
>
> FAILED CONTIG:Chr06
>
>
> Thanks
>
> Kapeel
> --
>
>
>
> *Kapeel ChouguleComputational Scientist Developer II*
>
>
> *One Bungtown Road Cold Spring Harbor, NY 11724http://www.warelab.org/
> <http://www.warelab.org/>*
> <Chr06.gff><maker_opts.ctl><maker.run.log>________________
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>
>
>
>
>


-- 



*Kapeel ChouguleComputational Scientist Developer II*


*One Bungtown Road Cold Spring Harbor, NY 11724http://www.warelab.org/
<http://www.warelab.org/>*
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