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

[Carson Holt]

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 <http://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 Chougule
> Computational Scientist Developer II
> One Bungtown Road Cold Spring Harbor, NY 11724
> http://www.warelab.org/ <http://www.warelab.org/>
> 
> <Chr06.gff><maker_opts.ctl><maker.run.log>_______________________________________________
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